Starting phenix.real_space_refine on Tue Aug 26 17:34:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fco_28988/08_2025/8fco_28988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fco_28988/08_2025/8fco_28988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fco_28988/08_2025/8fco_28988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fco_28988/08_2025/8fco_28988.map" model { file = "/net/cci-nas-00/data/ceres_data/8fco_28988/08_2025/8fco_28988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fco_28988/08_2025/8fco_28988.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 197 5.16 5 C 24846 2.51 5 N 6943 2.21 5 O 7559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39569 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "B" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 Chain: "H" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.08, per 1000 atoms: 0.23 Number of scatterers: 39569 At special positions: 0 Unit cell: (214.338, 193.488, 115.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 197 16.00 P 24 15.00 O 7559 8.00 N 6943 7.00 C 24846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9368 Finding SS restraints... Secondary structure from input PDB file: 263 helices and 42 sheets defined 52.4% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.054A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 4.073A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.582A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.692A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.615A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 570 removed outlier: 4.075A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.570A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.882A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.507A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.553A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.123A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 431 removed outlier: 4.362A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.976A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 609 Processing helix chain 'B' and resid 610 through 611 No H-bonds generated for 'chain 'B' and resid 610 through 611' Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.651A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 707 Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.515A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'H' and resid 50 through 68 Processing helix chain 'H' and resid 136 through 149 removed outlier: 3.739A pdb=" N PHE H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 165 removed outlier: 4.061A pdb=" N ASN H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 188 removed outlier: 3.511A pdb=" N ILE H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 194 Processing helix chain 'H' and resid 201 through 208 Processing helix chain 'H' and resid 213 through 221 Processing helix chain 'H' and resid 243 through 248 Processing helix chain 'H' and resid 250 through 262 Processing helix chain 'H' and resid 281 through 285 Processing helix chain 'H' and resid 296 through 316 Processing helix chain 'H' and resid 319 through 328 Processing helix chain 'H' and resid 329 through 331 No H-bonds generated for 'chain 'H' and resid 329 through 331' Processing helix chain 'H' and resid 358 through 370 removed outlier: 3.881A pdb=" N VAL H 362 " --> pdb=" O ARG H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 421 removed outlier: 3.595A pdb=" N ASP H 417 " --> pdb=" O ALA H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 435 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.641A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 4.080A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.665A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.654A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.516A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.154A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.509A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 120 through 123 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.720A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.500A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.725A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.073A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.565A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.616A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.880A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.206A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 Processing helix chain 'F' and resid 610 through 611 No H-bonds generated for 'chain 'F' and resid 610 through 611' Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.689A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.500A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.824A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.638A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.876A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.077A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 4.833A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.530A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.506A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.874A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 706 removed outlier: 3.683A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 Processing helix chain 'E' and resid 748 through 762 removed outlier: 4.169A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.810A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.100A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.691A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 3.560A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 431 " --> pdb=" O MET D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.505A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.873A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 706 removed outlier: 3.698A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 removed outlier: 4.281A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.803A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 165 removed outlier: 4.120A pdb=" N ASN G 165 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 188 Processing helix chain 'G' and resid 191 through 194 Processing helix chain 'G' and resid 201 through 208 Processing helix chain 'G' and resid 213 through 221 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 249 through 262 removed outlier: 4.419A pdb=" N LEU G 253 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.541A pdb=" N SER G 284 " --> pdb=" O PRO G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 294 removed outlier: 4.346A pdb=" N PHE G 293 " --> pdb=" O GLY G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 316 Processing helix chain 'G' and resid 319 through 329 removed outlier: 3.908A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.905A pdb=" N VAL G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 369 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 421 removed outlier: 3.577A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.377A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.617A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.810A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.135A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.513A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 29 Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.684A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.386A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.593A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 131 through 133 Processing sheet with id=AB5, first strand: chain 'H' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'H' and resid 386 through 387 removed outlier: 4.238A pdb=" N LEU H 379 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ALA H 404 " --> pdb=" O TYR H 336 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU H 338 " --> pdb=" O ALA H 404 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU H 406 " --> pdb=" O LEU H 338 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG H 340 " --> pdb=" O LEU H 406 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE H 408 " --> pdb=" O ARG H 340 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG H 342 " --> pdb=" O PHE H 408 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N TRP H 410 " --> pdb=" O ARG H 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 25 through 30 removed outlier: 6.491A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 55 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.680A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AC1, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.694A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.171A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.498A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.380A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.673A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AC7, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AC8, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.087A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.502A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.970A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.955A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AD4, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.806A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.260A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.470A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 25 through 29 removed outlier: 7.731A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP D 74 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 41 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.607A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AE1, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AE2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.155A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.388A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AE5, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AE6, first strand: chain 'G' and resid 386 through 387 removed outlier: 4.612A pdb=" N LEU G 379 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ALA G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU G 338 " --> pdb=" O ALA G 404 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU G 406 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG G 340 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE G 408 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG G 342 " --> pdb=" O PHE G 408 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N TRP G 410 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 276 " --> pdb=" O GLU G 438 " (cutoff:3.500A) 1863 hydrogen bonds defined for protein. 5226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.62 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8204 1.33 - 1.45: 8363 1.45 - 1.57: 23320 1.57 - 1.69: 36 1.69 - 1.81: 312 Bond restraints: 40235 Sorted by residual: bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 40230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 53121 2.48 - 4.96: 1129 4.96 - 7.44: 108 7.44 - 9.92: 31 9.92 - 12.40: 11 Bond angle restraints: 54400 Sorted by residual: angle pdb=" N LEU H 331 " pdb=" CA LEU H 331 " pdb=" C LEU H 331 " ideal model delta sigma weight residual 113.28 123.94 -10.66 1.22e+00 6.72e-01 7.63e+01 angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.50 123.95 -10.45 1.23e+00 6.61e-01 7.21e+01 angle pdb=" N ARG H 332 " pdb=" CA ARG H 332 " pdb=" C ARG H 332 " ideal model delta sigma weight residual 112.41 122.50 -10.09 1.30e+00 5.92e-01 6.02e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 113.17 122.40 -9.23 1.26e+00 6.30e-01 5.36e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 111.82 118.40 -6.58 1.16e+00 7.43e-01 3.22e+01 ... (remaining 54395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 24600 35.89 - 71.77: 258 71.77 - 107.66: 40 107.66 - 143.55: 9 143.55 - 179.43: 7 Dihedral angle restraints: 24914 sinusoidal: 10480 harmonic: 14434 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 119.43 -179.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 118.43 -178.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 116.88 -176.88 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 24911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4378 0.048 - 0.096: 1065 0.096 - 0.144: 493 0.144 - 0.192: 185 0.192 - 0.240: 12 Chirality restraints: 6133 Sorted by residual: chirality pdb=" CA ILE B 590 " pdb=" N ILE B 590 " pdb=" C ILE B 590 " pdb=" CB ILE B 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE C 590 " pdb=" N ILE C 590 " pdb=" C ILE C 590 " pdb=" CB ILE C 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE A 590 " pdb=" N ILE A 590 " pdb=" C ILE A 590 " pdb=" CB ILE A 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 6130 not shown) Planarity restraints: 7130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 534 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.36e+00 pdb=" C GLU F 534 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU F 534 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C GLU G 254 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU G 254 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG G 255 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 254 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C GLU H 254 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU H 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG H 255 " -0.013 2.00e-02 2.50e+03 ... (remaining 7127 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 13505 2.87 - 3.37: 37586 3.37 - 3.88: 67051 3.88 - 4.39: 77583 4.39 - 4.90: 127123 Nonbonded interactions: 322848 Sorted by model distance: nonbonded pdb=" OD2 ASP D 368 " pdb=" NZ LYS D 565 " model vdw 2.358 3.120 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.399 3.120 nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.399 3.120 nonbonded pdb=" NZ LYS B 512 " pdb=" O GLY B 637 " model vdw 2.414 3.120 nonbonded pdb=" OD2 ASP G 176 " pdb=" NZ LYS G 180 " model vdw 2.419 3.120 ... (remaining 322843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 499 or resid 509 through 902)) selection = chain 'B' selection = (chain 'C' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'F' and (resid 23 through 499 or resid 509 through 902)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.010 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.110 40235 Z= 0.624 Angle : 0.890 12.403 54400 Z= 0.561 Chirality : 0.058 0.240 6133 Planarity : 0.004 0.035 7130 Dihedral : 12.140 179.435 15546 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.11), residues: 4965 helix: -0.18 (0.10), residues: 2216 sheet: 0.64 (0.16), residues: 881 loop : 0.93 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 745 TYR 0.001 0.000 TYR H 334 PHE 0.001 0.000 PHE C 363 TRP 0.001 0.000 TRP C 476 HIS 0.001 0.000 HIS H 256 Details of bonding type rmsd covalent geometry : bond 0.01090 (40235) covalent geometry : angle 0.89013 (54400) hydrogen bonds : bond 0.21189 ( 1863) hydrogen bonds : angle 6.51354 ( 5226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1473 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 506 PHE cc_start: 0.5812 (m-80) cc_final: 0.5561 (m-10) REVERT: C 509 THR cc_start: 0.7074 (m) cc_final: 0.6727 (p) REVERT: H 408 PHE cc_start: 0.6370 (t80) cc_final: 0.5951 (t80) REVERT: A 219 MET cc_start: 0.8052 (mtm) cc_final: 0.7756 (mtp) REVERT: A 427 MET cc_start: 0.4983 (mtp) cc_final: 0.3988 (mtp) REVERT: D 432 LEU cc_start: 0.4168 (tt) cc_final: 0.3861 (tt) REVERT: D 630 ASP cc_start: 0.5562 (t0) cc_final: 0.5301 (t70) outliers start: 0 outliers final: 0 residues processed: 1473 average time/residue: 0.2372 time to fit residues: 537.7606 Evaluate side-chains 686 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 327 GLN C 348 ASN C 603 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 443 ASN B 490 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN A 183 HIS A 215 GLN A 404 HIS A 406 HIS A 602 ASN F 115 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 460 ASN F 494 GLN F 603 GLN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 90 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 GLN D 421 GLN D 460 ASN D 602 ASN D 603 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.161890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115285 restraints weight = 71820.017| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.65 r_work: 0.3435 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40235 Z= 0.182 Angle : 0.705 10.711 54400 Z= 0.350 Chirality : 0.047 0.214 6133 Planarity : 0.005 0.057 7130 Dihedral : 9.884 177.978 5554 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Rotamer: Outliers : 2.80 % Allowed : 9.89 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.12), residues: 4965 helix: 0.98 (0.11), residues: 2256 sheet: 0.60 (0.16), residues: 882 loop : 1.07 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 274 TYR 0.031 0.002 TYR E 755 PHE 0.023 0.002 PHE D 516 TRP 0.015 0.002 TRP A 551 HIS 0.009 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00418 (40235) covalent geometry : angle 0.70541 (54400) hydrogen bonds : bond 0.05361 ( 1863) hydrogen bonds : angle 4.66460 ( 5226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 725 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 226 HIS cc_start: 0.8014 (m-70) cc_final: 0.7793 (m-70) REVERT: C 309 ILE cc_start: 0.8811 (tt) cc_final: 0.8537 (tt) REVERT: C 426 LYS cc_start: 0.8502 (tttt) cc_final: 0.8284 (tmmt) REVERT: C 506 PHE cc_start: 0.8730 (m-80) cc_final: 0.8404 (m-10) REVERT: C 598 ASP cc_start: 0.4878 (t0) cc_final: 0.4162 (p0) REVERT: B 173 TYR cc_start: 0.8759 (p90) cc_final: 0.8402 (p90) REVERT: B 221 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: B 352 SER cc_start: 0.8657 (m) cc_final: 0.8382 (p) REVERT: H 412 MET cc_start: 0.7135 (mtt) cc_final: 0.6792 (mtm) REVERT: A 35 ASP cc_start: 0.8400 (t0) cc_final: 0.7951 (t70) REVERT: A 219 MET cc_start: 0.8526 (mtm) cc_final: 0.8323 (mtp) REVERT: A 427 MET cc_start: 0.7355 (mtp) cc_final: 0.6970 (mtp) REVERT: A 442 MET cc_start: 0.8876 (tpt) cc_final: 0.8673 (tpt) REVERT: A 483 GLU cc_start: 0.7964 (mp0) cc_final: 0.7253 (pt0) REVERT: A 487 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.6745 (ptp-170) REVERT: A 755 TYR cc_start: 0.5063 (m-80) cc_final: 0.4738 (m-80) REVERT: F 487 ARG cc_start: 0.8856 (ttp-110) cc_final: 0.8502 (mtp-110) REVERT: F 603 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: E 427 MET cc_start: 0.7507 (mmm) cc_final: 0.7242 (mmm) REVERT: E 564 ASP cc_start: 0.8604 (m-30) cc_final: 0.8378 (m-30) REVERT: E 614 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8062 (mmmm) REVERT: E 625 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7464 (mmp-170) REVERT: E 641 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: E 729 PRO cc_start: 0.7495 (Cg_exo) cc_final: 0.7219 (Cg_endo) REVERT: D 46 MET cc_start: 0.6081 (ptt) cc_final: 0.5811 (ppp) REVERT: D 51 LEU cc_start: 0.7372 (mm) cc_final: 0.6999 (mm) REVERT: D 52 PHE cc_start: 0.7636 (m-80) cc_final: 0.6361 (t80) REVERT: D 74 ASP cc_start: 0.7459 (t0) cc_final: 0.6974 (t0) REVERT: D 322 ARG cc_start: 0.7380 (ttm110) cc_final: 0.6929 (ptt-90) REVERT: D 442 MET cc_start: 0.8533 (mmm) cc_final: 0.8276 (mmm) REVERT: D 488 GLU cc_start: 0.8691 (tp30) cc_final: 0.8266 (tt0) REVERT: D 509 THR cc_start: 0.8808 (t) cc_final: 0.8588 (p) REVERT: D 577 ASP cc_start: 0.8401 (t0) cc_final: 0.8193 (t0) REVERT: D 605 LEU cc_start: 0.9109 (mt) cc_final: 0.8512 (mt) REVERT: D 608 MET cc_start: 0.8932 (mtp) cc_final: 0.8507 (mtm) outliers start: 119 outliers final: 75 residues processed: 810 average time/residue: 0.2086 time to fit residues: 275.8920 Evaluate side-chains 641 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 563 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 663 LYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 603 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 641 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 603 GLN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 343 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 409 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 435 optimal weight: 1.9990 chunk 425 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 407 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN C 199 ASN C 327 GLN C 351 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 443 ASN B 460 ASN B 603 GLN B 616 ASN H 294 ASN A 404 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 340 HIS D 33 ASN D 460 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.159518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.115023 restraints weight = 71427.406| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.23 r_work: 0.3424 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40235 Z= 0.147 Angle : 0.645 9.787 54400 Z= 0.312 Chirality : 0.045 0.269 6133 Planarity : 0.004 0.074 7130 Dihedral : 9.393 179.110 5554 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.63 % Allowed : 11.58 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.12), residues: 4965 helix: 1.24 (0.11), residues: 2256 sheet: 0.54 (0.17), residues: 872 loop : 0.96 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 113 TYR 0.022 0.002 TYR C 244 PHE 0.025 0.001 PHE F 52 TRP 0.012 0.001 TRP C 551 HIS 0.011 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00336 (40235) covalent geometry : angle 0.64473 (54400) hydrogen bonds : bond 0.04446 ( 1863) hydrogen bonds : angle 4.41611 ( 5226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 633 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 VAL cc_start: 0.7981 (t) cc_final: 0.7680 (p) REVERT: C 123 VAL cc_start: 0.7251 (t) cc_final: 0.7006 (p) REVERT: C 309 ILE cc_start: 0.8716 (tt) cc_final: 0.8453 (tt) REVERT: C 506 PHE cc_start: 0.8776 (m-80) cc_final: 0.8540 (m-10) REVERT: C 508 MET cc_start: 0.8466 (ttt) cc_final: 0.7887 (ttt) REVERT: C 562 ILE cc_start: 0.8482 (mm) cc_final: 0.8097 (pt) REVERT: B 75 ASP cc_start: 0.7036 (t0) cc_final: 0.6793 (t0) REVERT: B 173 TYR cc_start: 0.8628 (p90) cc_final: 0.8407 (p90) REVERT: B 221 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: B 352 SER cc_start: 0.8648 (m) cc_final: 0.8346 (p) REVERT: B 542 ILE cc_start: 0.7777 (mt) cc_final: 0.7397 (mt) REVERT: B 578 GLU cc_start: 0.7941 (tp30) cc_final: 0.7492 (tp30) REVERT: H 159 MET cc_start: 0.0564 (mmm) cc_final: -0.0131 (tpt) REVERT: H 363 TYR cc_start: 0.6901 (m-80) cc_final: 0.6473 (t80) REVERT: H 411 ASP cc_start: 0.6613 (t70) cc_final: 0.5909 (m-30) REVERT: A 35 ASP cc_start: 0.8469 (t0) cc_final: 0.7957 (t70) REVERT: A 150 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: A 278 LEU cc_start: 0.8231 (pp) cc_final: 0.7527 (mp) REVERT: A 383 ILE cc_start: 0.9132 (mt) cc_final: 0.8927 (mm) REVERT: A 427 MET cc_start: 0.7279 (mtp) cc_final: 0.6637 (mtp) REVERT: A 449 MET cc_start: 0.7880 (tpp) cc_final: 0.7498 (tpp) REVERT: A 498 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 499 HIS cc_start: 0.8041 (m-70) cc_final: 0.7742 (m-70) REVERT: A 577 ASP cc_start: 0.9348 (t0) cc_final: 0.9139 (t0) REVERT: F 55 ASP cc_start: 0.7911 (t0) cc_final: 0.7614 (m-30) REVERT: F 76 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8538 (m) REVERT: F 244 TYR cc_start: 0.9062 (p90) cc_final: 0.8797 (p90) REVERT: F 265 PHE cc_start: 0.7783 (m-80) cc_final: 0.7542 (m-80) REVERT: F 449 MET cc_start: 0.8136 (tpp) cc_final: 0.7721 (tpp) REVERT: F 487 ARG cc_start: 0.8893 (ttp-110) cc_final: 0.8621 (mtm110) REVERT: F 495 TYR cc_start: 0.8947 (m-10) cc_final: 0.8672 (m-80) REVERT: F 603 GLN cc_start: 0.8113 (mt0) cc_final: 0.7549 (mt0) REVERT: E 491 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8034 (mp0) REVERT: E 517 TYR cc_start: 0.8666 (p90) cc_final: 0.8333 (p90) REVERT: E 564 ASP cc_start: 0.8731 (m-30) cc_final: 0.8330 (m-30) REVERT: E 567 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8398 (ttm-80) REVERT: E 614 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8102 (mmmm) REVERT: E 625 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7543 (mmp-170) REVERT: E 691 CYS cc_start: 0.8502 (m) cc_final: 0.8146 (t) REVERT: D 46 MET cc_start: 0.6180 (ptt) cc_final: 0.5897 (ppp) REVERT: D 51 LEU cc_start: 0.7468 (mm) cc_final: 0.7024 (mm) REVERT: D 52 PHE cc_start: 0.7776 (m-80) cc_final: 0.6466 (t80) REVERT: D 74 ASP cc_start: 0.7481 (t0) cc_final: 0.7012 (t0) REVERT: D 98 ASP cc_start: 0.8086 (m-30) cc_final: 0.7784 (m-30) REVERT: D 124 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7204 (mp0) REVERT: D 319 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7883 (mm-30) REVERT: D 322 ARG cc_start: 0.7402 (ttm110) cc_final: 0.6959 (ptt-90) REVERT: D 470 GLU cc_start: 0.8241 (pm20) cc_final: 0.7777 (pt0) REVERT: D 577 ASP cc_start: 0.8366 (t0) cc_final: 0.8080 (t0) REVERT: D 605 LEU cc_start: 0.9073 (mt) cc_final: 0.8509 (mt) REVERT: D 608 MET cc_start: 0.8885 (mtp) cc_final: 0.8461 (mtm) REVERT: G 54 MET cc_start: 0.5414 (tpp) cc_final: 0.5202 (tpp) REVERT: G 299 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8472 (mp0) outliers start: 112 outliers final: 79 residues processed: 712 average time/residue: 0.1965 time to fit residues: 231.4789 Evaluate side-chains 626 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 544 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 431 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 405 optimal weight: 3.9990 chunk 113 optimal weight: 0.1980 chunk 491 optimal weight: 9.9990 chunk 472 optimal weight: 40.0000 chunk 177 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 494 GLN B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN H 285 GLN H 294 ASN A 183 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS F 327 GLN F 348 ASN F 460 ASN E 115 HIS E 183 HIS E 285 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS D 199 ASN D 327 GLN D 421 GLN D 460 ASN G 278 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.150965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105818 restraints weight = 72433.048| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.28 r_work: 0.3315 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 40235 Z= 0.284 Angle : 0.749 11.875 54400 Z= 0.368 Chirality : 0.049 0.229 6133 Planarity : 0.006 0.089 7130 Dihedral : 9.313 177.861 5554 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.69 % Allowed : 12.81 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.12), residues: 4965 helix: 1.02 (0.11), residues: 2252 sheet: 0.32 (0.17), residues: 855 loop : 0.49 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 741 TYR 0.022 0.003 TYR C 244 PHE 0.029 0.002 PHE D 674 TRP 0.012 0.002 TRP C 476 HIS 0.010 0.002 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00670 (40235) covalent geometry : angle 0.74910 (54400) hydrogen bonds : bond 0.04753 ( 1863) hydrogen bonds : angle 4.63742 ( 5226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 573 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 VAL cc_start: 0.7694 (t) cc_final: 0.7475 (p) REVERT: C 203 TYR cc_start: 0.8456 (m-80) cc_final: 0.8130 (m-80) REVERT: C 309 ILE cc_start: 0.8769 (tt) cc_final: 0.8446 (tt) REVERT: C 315 LYS cc_start: 0.6790 (mmtt) cc_final: 0.6586 (pttt) REVERT: C 426 LYS cc_start: 0.8517 (tttt) cc_final: 0.8284 (mtmm) REVERT: C 442 MET cc_start: 0.8774 (mmm) cc_final: 0.8571 (tpp) REVERT: C 506 PHE cc_start: 0.8648 (m-80) cc_final: 0.8387 (m-10) REVERT: C 562 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8349 (pt) REVERT: C 577 ASP cc_start: 0.8451 (t0) cc_final: 0.8092 (t0) REVERT: B 75 ASP cc_start: 0.7276 (t0) cc_final: 0.6940 (t0) REVERT: B 275 MET cc_start: 0.8603 (mmm) cc_final: 0.8296 (mmt) REVERT: B 352 SER cc_start: 0.8739 (m) cc_final: 0.8405 (t) REVERT: B 578 GLU cc_start: 0.8210 (tp30) cc_final: 0.7823 (tp30) REVERT: B 671 ASP cc_start: 0.8183 (t0) cc_final: 0.7888 (t70) REVERT: H 274 ARG cc_start: 0.7874 (tmm-80) cc_final: 0.7454 (ptm160) REVERT: H 354 TYR cc_start: 0.7834 (m-80) cc_final: 0.6811 (m-80) REVERT: H 407 THR cc_start: 0.7608 (m) cc_final: 0.7399 (p) REVERT: A 35 ASP cc_start: 0.8583 (t0) cc_final: 0.8124 (t70) REVERT: A 150 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: A 442 MET cc_start: 0.9092 (tpt) cc_final: 0.8533 (tpt) REVERT: A 449 MET cc_start: 0.8041 (tpp) cc_final: 0.7600 (tpp) REVERT: A 483 GLU cc_start: 0.8481 (pm20) cc_final: 0.7959 (pt0) REVERT: F 190 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8824 (mttp) REVERT: F 603 GLN cc_start: 0.8281 (mt0) cc_final: 0.7743 (mt0) REVERT: F 742 PHE cc_start: 0.8217 (m-80) cc_final: 0.7921 (m-80) REVERT: E 230 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8003 (t80) REVERT: E 459 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8800 (p) REVERT: E 491 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8037 (mp0) REVERT: E 517 TYR cc_start: 0.9083 (p90) cc_final: 0.8794 (p90) REVERT: E 564 ASP cc_start: 0.9028 (m-30) cc_final: 0.8563 (m-30) REVERT: E 567 ARG cc_start: 0.8789 (mtp-110) cc_final: 0.8489 (ttm-80) REVERT: E 614 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8168 (mmmm) REVERT: E 625 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7706 (mmp-170) REVERT: D 46 MET cc_start: 0.6144 (ptt) cc_final: 0.5861 (ppp) REVERT: D 74 ASP cc_start: 0.7836 (t0) cc_final: 0.7275 (t0) REVERT: D 113 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6899 (ptm-80) REVERT: D 319 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 322 ARG cc_start: 0.7408 (ttm110) cc_final: 0.7004 (ptt-90) REVERT: D 453 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8044 (mtm180) REVERT: D 577 ASP cc_start: 0.8432 (t0) cc_final: 0.8052 (t0) REVERT: D 605 LEU cc_start: 0.9172 (mt) cc_final: 0.8964 (mt) REVERT: D 630 ASP cc_start: 0.8083 (t70) cc_final: 0.7238 (t0) REVERT: D 680 ASN cc_start: 0.7861 (t0) cc_final: 0.7633 (t0) REVERT: D 682 PHE cc_start: 0.7275 (m-80) cc_final: 0.6877 (m-80) REVERT: G 54 MET cc_start: 0.5727 (tpp) cc_final: 0.5524 (tpp) REVERT: G 159 MET cc_start: -0.0484 (ttm) cc_final: -0.0801 (mmm) outliers start: 157 outliers final: 102 residues processed: 686 average time/residue: 0.2031 time to fit residues: 228.9886 Evaluate side-chains 618 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 510 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 6 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 425 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 356 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN H 294 ASN A 183 HIS ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 460 ASN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110707 restraints weight = 71952.129| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.21 r_work: 0.3362 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40235 Z= 0.129 Angle : 0.622 9.983 54400 Z= 0.300 Chirality : 0.045 0.228 6133 Planarity : 0.005 0.082 7130 Dihedral : 8.817 176.493 5554 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.58 % Allowed : 14.45 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.12), residues: 4965 helix: 1.27 (0.11), residues: 2262 sheet: 0.37 (0.17), residues: 863 loop : 0.72 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 338 TYR 0.021 0.002 TYR C 244 PHE 0.021 0.001 PHE B 52 TRP 0.014 0.001 TRP C 476 HIS 0.007 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00296 (40235) covalent geometry : angle 0.62245 (54400) hydrogen bonds : bond 0.03875 ( 1863) hydrogen bonds : angle 4.32936 ( 5226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 594 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 VAL cc_start: 0.7985 (t) cc_final: 0.7766 (p) REVERT: C 123 VAL cc_start: 0.7631 (t) cc_final: 0.7409 (p) REVERT: C 309 ILE cc_start: 0.8658 (tt) cc_final: 0.8356 (tt) REVERT: C 426 LYS cc_start: 0.8486 (tttt) cc_final: 0.8175 (mtmm) REVERT: C 442 MET cc_start: 0.8712 (mmm) cc_final: 0.8508 (tpp) REVERT: C 506 PHE cc_start: 0.8681 (m-80) cc_final: 0.8455 (m-10) REVERT: C 562 ILE cc_start: 0.8674 (mm) cc_final: 0.8203 (pt) REVERT: B 59 LEU cc_start: 0.8800 (mt) cc_final: 0.8428 (mt) REVERT: B 75 ASP cc_start: 0.7205 (t0) cc_final: 0.6932 (t0) REVERT: B 352 SER cc_start: 0.8679 (m) cc_final: 0.8339 (t) REVERT: B 578 GLU cc_start: 0.8113 (tp30) cc_final: 0.7705 (tp30) REVERT: B 608 MET cc_start: 0.8067 (mtm) cc_final: 0.7837 (mtm) REVERT: H 159 MET cc_start: 0.0672 (mmm) cc_final: 0.0047 (tpt) REVERT: H 274 ARG cc_start: 0.7912 (tmm-80) cc_final: 0.7414 (ptm160) REVERT: H 342 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7061 (mtt-85) REVERT: H 354 TYR cc_start: 0.7745 (m-80) cc_final: 0.6654 (m-80) REVERT: H 407 THR cc_start: 0.7539 (m) cc_final: 0.6892 (t) REVERT: A 35 ASP cc_start: 0.8575 (t0) cc_final: 0.8000 (t70) REVERT: A 63 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8466 (mttm) REVERT: A 150 ASP cc_start: 0.7568 (t0) cc_final: 0.7296 (m-30) REVERT: A 442 MET cc_start: 0.9119 (tpt) cc_final: 0.8665 (tpt) REVERT: A 449 MET cc_start: 0.7872 (tpp) cc_final: 0.7287 (tpp) REVERT: A 466 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: F 190 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8784 (mttp) REVERT: F 192 GLU cc_start: 0.7840 (mp0) cc_final: 0.7422 (mp0) REVERT: F 449 MET cc_start: 0.8290 (tpp) cc_final: 0.7426 (tpp) REVERT: F 487 ARG cc_start: 0.8924 (ttp-110) cc_final: 0.8567 (mtp-110) REVERT: F 603 GLN cc_start: 0.8155 (mt0) cc_final: 0.7441 (mt0) REVERT: F 742 PHE cc_start: 0.8151 (m-80) cc_final: 0.7849 (m-80) REVERT: E 230 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7740 (t80) REVERT: E 352 SER cc_start: 0.8727 (m) cc_final: 0.8525 (p) REVERT: E 491 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7999 (mp0) REVERT: E 517 TYR cc_start: 0.9068 (p90) cc_final: 0.8759 (p90) REVERT: E 564 ASP cc_start: 0.8979 (m-30) cc_final: 0.8597 (m-30) REVERT: E 567 ARG cc_start: 0.8711 (mtp-110) cc_final: 0.8438 (ttm-80) REVERT: E 625 ARG cc_start: 0.8080 (tpp-160) cc_final: 0.7675 (mmp-170) REVERT: E 700 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7324 (ttp80) REVERT: E 740 MET cc_start: 0.8524 (tpt) cc_final: 0.8277 (tpt) REVERT: E 756 GLU cc_start: 0.8518 (tp30) cc_final: 0.8013 (pp20) REVERT: D 46 MET cc_start: 0.6082 (ptt) cc_final: 0.5827 (ppp) REVERT: D 52 PHE cc_start: 0.7814 (m-80) cc_final: 0.6347 (t80) REVERT: D 74 ASP cc_start: 0.7734 (t0) cc_final: 0.7268 (t0) REVERT: D 319 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7811 (mm-30) REVERT: D 322 ARG cc_start: 0.7335 (ttm110) cc_final: 0.6960 (ttp-110) REVERT: D 383 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9269 (mt) REVERT: D 453 ARG cc_start: 0.8327 (mtm180) cc_final: 0.8087 (mtm180) REVERT: D 577 ASP cc_start: 0.8433 (t0) cc_final: 0.8058 (t0) REVERT: D 605 LEU cc_start: 0.9112 (mt) cc_final: 0.8571 (mt) REVERT: D 608 MET cc_start: 0.8723 (mtp) cc_final: 0.8430 (mtm) REVERT: D 630 ASP cc_start: 0.8040 (t70) cc_final: 0.7115 (t0) REVERT: G 54 MET cc_start: 0.5661 (tpp) cc_final: 0.5403 (tpp) REVERT: G 159 MET cc_start: -0.0594 (ttm) cc_final: -0.0925 (mmm) REVERT: G 324 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8503 (mm-30) outliers start: 110 outliers final: 76 residues processed: 670 average time/residue: 0.2045 time to fit residues: 225.1362 Evaluate side-chains 610 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 531 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 424 optimal weight: 0.2980 chunk 272 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 538 ASN F 602 ASN F 641 GLN E 183 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117523 restraints weight = 72349.875| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.03 r_work: 0.3374 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 40235 Z= 0.133 Angle : 0.619 10.337 54400 Z= 0.295 Chirality : 0.044 0.205 6133 Planarity : 0.004 0.078 7130 Dihedral : 8.416 175.521 5554 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.01 % Allowed : 14.69 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.12), residues: 4965 helix: 1.36 (0.11), residues: 2265 sheet: 0.39 (0.17), residues: 855 loop : 0.73 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 732 TYR 0.017 0.001 TYR C 244 PHE 0.017 0.001 PHE D 742 TRP 0.017 0.001 TRP C 476 HIS 0.010 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00309 (40235) covalent geometry : angle 0.61873 (54400) hydrogen bonds : bond 0.03703 ( 1863) hydrogen bonds : angle 4.27745 ( 5226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 570 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 VAL cc_start: 0.7639 (t) cc_final: 0.7402 (p) REVERT: C 309 ILE cc_start: 0.8669 (tt) cc_final: 0.8351 (tt) REVERT: C 426 LYS cc_start: 0.8435 (tttt) cc_final: 0.8090 (mtmm) REVERT: C 464 LEU cc_start: 0.9068 (tp) cc_final: 0.8531 (mt) REVERT: C 506 PHE cc_start: 0.8680 (m-80) cc_final: 0.8466 (m-10) REVERT: C 562 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8305 (pt) REVERT: B 75 ASP cc_start: 0.7099 (t0) cc_final: 0.6762 (t0) REVERT: B 352 SER cc_start: 0.8686 (m) cc_final: 0.8331 (t) REVERT: B 578 GLU cc_start: 0.8119 (tp30) cc_final: 0.7669 (tp30) REVERT: H 159 MET cc_start: 0.0691 (mmm) cc_final: 0.0011 (tpt) REVERT: H 274 ARG cc_start: 0.7993 (tmm-80) cc_final: 0.7420 (ptm160) REVERT: H 354 TYR cc_start: 0.7776 (m-80) cc_final: 0.6678 (m-80) REVERT: H 363 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6553 (t80) REVERT: H 407 THR cc_start: 0.7547 (m) cc_final: 0.6849 (t) REVERT: A 35 ASP cc_start: 0.8615 (t0) cc_final: 0.8077 (t70) REVERT: A 63 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8448 (mttm) REVERT: A 150 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: A 438 ASP cc_start: 0.8660 (t0) cc_final: 0.8233 (t70) REVERT: A 442 MET cc_start: 0.9109 (tpt) cc_final: 0.8707 (tpt) REVERT: A 466 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: A 483 GLU cc_start: 0.8543 (pm20) cc_final: 0.8059 (pt0) REVERT: A 577 ASP cc_start: 0.9223 (t0) cc_final: 0.9000 (t0) REVERT: A 755 TYR cc_start: 0.5567 (m-80) cc_final: 0.5358 (m-80) REVERT: F 190 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8746 (mttp) REVERT: F 449 MET cc_start: 0.8294 (tpp) cc_final: 0.7558 (tpp) REVERT: F 487 ARG cc_start: 0.8906 (ttp-110) cc_final: 0.8549 (mtp-110) REVERT: F 603 GLN cc_start: 0.8003 (mt0) cc_final: 0.7560 (mt0) REVERT: E 230 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8035 (t80) REVERT: E 491 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7996 (mp0) REVERT: E 517 TYR cc_start: 0.9089 (p90) cc_final: 0.8759 (p90) REVERT: E 564 ASP cc_start: 0.8979 (m-30) cc_final: 0.8644 (m-30) REVERT: E 567 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.8472 (ttm-80) REVERT: E 625 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7752 (mmp-170) REVERT: E 700 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7372 (ttp80) REVERT: E 740 MET cc_start: 0.8515 (tpt) cc_final: 0.8258 (tpt) REVERT: D 46 MET cc_start: 0.6081 (ptt) cc_final: 0.5836 (ppp) REVERT: D 52 PHE cc_start: 0.7825 (m-80) cc_final: 0.6351 (t80) REVERT: D 74 ASP cc_start: 0.7728 (t0) cc_final: 0.7308 (t0) REVERT: D 221 GLU cc_start: 0.8817 (pp20) cc_final: 0.8375 (pp20) REVERT: D 319 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7472 (mm-30) REVERT: D 322 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6996 (ttp-170) REVERT: D 383 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9222 (mt) REVERT: D 453 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8122 (mtm180) REVERT: D 556 GLU cc_start: 0.7461 (pm20) cc_final: 0.7106 (pt0) REVERT: D 577 ASP cc_start: 0.8433 (t0) cc_final: 0.8040 (t0) REVERT: D 605 LEU cc_start: 0.9108 (mt) cc_final: 0.8537 (mt) REVERT: D 608 MET cc_start: 0.8731 (mtp) cc_final: 0.8445 (mtm) REVERT: D 630 ASP cc_start: 0.8029 (t70) cc_final: 0.7235 (t0) REVERT: G 54 MET cc_start: 0.5763 (tpp) cc_final: 0.5517 (tpp) REVERT: G 159 MET cc_start: -0.0687 (ttm) cc_final: -0.1029 (mmm) outliers start: 128 outliers final: 85 residues processed: 660 average time/residue: 0.1913 time to fit residues: 209.6553 Evaluate side-chains 627 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 535 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 625 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 386 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 473 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 394 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 382 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 475 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS F 443 ASN F 494 GLN F 750 ASN E 183 HIS D 199 ASN D 226 HIS ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.150034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107026 restraints weight = 72952.395| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.46 r_work: 0.3264 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 40235 Z= 0.273 Angle : 0.735 12.054 54400 Z= 0.357 Chirality : 0.048 0.274 6133 Planarity : 0.005 0.081 7130 Dihedral : 8.306 166.323 5554 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.43 % Allowed : 14.64 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.12), residues: 4965 helix: 1.09 (0.11), residues: 2255 sheet: 0.15 (0.17), residues: 842 loop : 0.32 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 349 TYR 0.023 0.002 TYR G 334 PHE 0.022 0.002 PHE F 552 TRP 0.025 0.002 TRP C 476 HIS 0.008 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00648 (40235) covalent geometry : angle 0.73532 (54400) hydrogen bonds : bond 0.04378 ( 1863) hydrogen bonds : angle 4.58072 ( 5226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 551 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 VAL cc_start: 0.7822 (t) cc_final: 0.7596 (p) REVERT: C 309 ILE cc_start: 0.8757 (tt) cc_final: 0.8404 (tt) REVERT: C 404 HIS cc_start: 0.8687 (t-90) cc_final: 0.8437 (t-90) REVERT: C 426 LYS cc_start: 0.8465 (tttt) cc_final: 0.8112 (mtmm) REVERT: C 464 LEU cc_start: 0.9035 (tp) cc_final: 0.8438 (mt) REVERT: B 75 ASP cc_start: 0.7409 (t0) cc_final: 0.7021 (t0) REVERT: B 221 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: B 317 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.4138 (p-80) REVERT: B 352 SER cc_start: 0.8792 (m) cc_final: 0.8396 (t) REVERT: B 578 GLU cc_start: 0.8234 (tp30) cc_final: 0.7756 (tp30) REVERT: B 757 MET cc_start: 0.7425 (ptm) cc_final: 0.7169 (ptt) REVERT: H 64 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6471 (tp30) REVERT: H 159 MET cc_start: 0.0626 (mmm) cc_final: 0.0116 (tpt) REVERT: H 274 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7392 (ptm160) REVERT: H 354 TYR cc_start: 0.7831 (m-80) cc_final: 0.6543 (m-80) REVERT: H 363 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6636 (t80) REVERT: H 407 THR cc_start: 0.7604 (m) cc_final: 0.6945 (t) REVERT: A 35 ASP cc_start: 0.8653 (t0) cc_final: 0.8117 (t70) REVERT: A 150 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: A 317 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.5798 (p-80) REVERT: A 352 SER cc_start: 0.9257 (m) cc_final: 0.8805 (t) REVERT: A 442 MET cc_start: 0.9151 (tpt) cc_final: 0.8735 (tpt) REVERT: A 466 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: A 483 GLU cc_start: 0.8533 (pm20) cc_final: 0.7967 (pt0) REVERT: A 543 LYS cc_start: 0.7723 (tppt) cc_final: 0.7435 (ttmm) REVERT: A 577 ASP cc_start: 0.9315 (t0) cc_final: 0.9059 (t0) REVERT: F 34 GLU cc_start: 0.8759 (pm20) cc_final: 0.8493 (mt-10) REVERT: F 190 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8790 (mttp) REVERT: F 449 MET cc_start: 0.8431 (tpp) cc_final: 0.8007 (tpp) REVERT: F 487 ARG cc_start: 0.8918 (ttp-110) cc_final: 0.8580 (mtp-110) REVERT: F 556 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: F 603 GLN cc_start: 0.8160 (mt0) cc_final: 0.7927 (mt0) REVERT: E 115 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7771 (t70) REVERT: E 230 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8188 (t80) REVERT: E 491 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8138 (tt0) REVERT: E 517 TYR cc_start: 0.9238 (p90) cc_final: 0.8899 (p90) REVERT: E 564 ASP cc_start: 0.9072 (m-30) cc_final: 0.8541 (m-30) REVERT: E 567 ARG cc_start: 0.8781 (mtp-110) cc_final: 0.8515 (ttm-80) REVERT: E 625 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.7703 (mmp-170) REVERT: E 700 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7404 (ttp80) REVERT: E 756 GLU cc_start: 0.8563 (tp30) cc_final: 0.7949 (pp20) REVERT: D 52 PHE cc_start: 0.7987 (m-80) cc_final: 0.6320 (t80) REVERT: D 74 ASP cc_start: 0.7884 (t0) cc_final: 0.7370 (t0) REVERT: D 319 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7549 (mm-30) REVERT: D 322 ARG cc_start: 0.7375 (ttm110) cc_final: 0.6995 (ttp-170) REVERT: D 436 THR cc_start: 0.7646 (p) cc_final: 0.6751 (p) REVERT: D 577 ASP cc_start: 0.8519 (t0) cc_final: 0.8119 (t0) REVERT: D 630 ASP cc_start: 0.8101 (t70) cc_final: 0.7278 (t0) REVERT: G 159 MET cc_start: -0.0768 (ttm) cc_final: -0.1114 (mmm) outliers start: 146 outliers final: 106 residues processed: 647 average time/residue: 0.2055 time to fit residues: 217.3882 Evaluate side-chains 616 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 501 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 625 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 699 ILE Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 142 optimal weight: 10.0000 chunk 361 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 484 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 495 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS F 602 ASN F 750 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 460 ASN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.154895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109922 restraints weight = 72492.066| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.25 r_work: 0.3334 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 40235 Z= 0.146 Angle : 0.648 11.452 54400 Z= 0.310 Chirality : 0.045 0.239 6133 Planarity : 0.005 0.082 7130 Dihedral : 7.676 164.850 5554 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.66 % Allowed : 15.72 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.12), residues: 4965 helix: 1.26 (0.11), residues: 2266 sheet: 0.17 (0.17), residues: 856 loop : 0.51 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 732 TYR 0.039 0.002 TYR H 336 PHE 0.019 0.001 PHE F 363 TRP 0.032 0.001 TRP C 476 HIS 0.007 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00342 (40235) covalent geometry : angle 0.64808 (54400) hydrogen bonds : bond 0.03756 ( 1863) hydrogen bonds : angle 4.35971 ( 5226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 548 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.7286 (pt0) cc_final: 0.6185 (tm-30) REVERT: C 123 VAL cc_start: 0.7787 (t) cc_final: 0.7559 (p) REVERT: C 162 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6944 (mt-10) REVERT: C 309 ILE cc_start: 0.8637 (tt) cc_final: 0.8297 (tt) REVERT: C 426 LYS cc_start: 0.8487 (tttt) cc_final: 0.8121 (mtmm) REVERT: C 464 LEU cc_start: 0.9059 (tp) cc_final: 0.8506 (mt) REVERT: B 75 ASP cc_start: 0.7273 (t0) cc_final: 0.6844 (t0) REVERT: B 229 LEU cc_start: 0.8008 (mm) cc_final: 0.7031 (tp) REVERT: B 352 SER cc_start: 0.8705 (m) cc_final: 0.8298 (t) REVERT: B 578 GLU cc_start: 0.8228 (tp30) cc_final: 0.7771 (tp30) REVERT: B 608 MET cc_start: 0.8285 (mtm) cc_final: 0.7426 (mtm) REVERT: B 757 MET cc_start: 0.7336 (ptm) cc_final: 0.7109 (ptt) REVERT: H 64 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6493 (tp30) REVERT: H 159 MET cc_start: 0.0920 (mmm) cc_final: 0.0344 (tpt) REVERT: H 274 ARG cc_start: 0.7957 (tmm-80) cc_final: 0.7375 (ptm160) REVERT: H 354 TYR cc_start: 0.7545 (m-80) cc_final: 0.6352 (m-80) REVERT: H 363 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6608 (t80) REVERT: H 407 THR cc_start: 0.7607 (m) cc_final: 0.6919 (t) REVERT: A 35 ASP cc_start: 0.8602 (t0) cc_final: 0.8028 (t70) REVERT: A 63 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8428 (mttm) REVERT: A 150 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 315 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8604 (mmtm) REVERT: A 317 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6496 (p-80) REVERT: A 352 SER cc_start: 0.9228 (m) cc_final: 0.8782 (t) REVERT: A 466 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: A 483 GLU cc_start: 0.8570 (pm20) cc_final: 0.7960 (pt0) REVERT: A 506 PHE cc_start: 0.8487 (m-80) cc_final: 0.8015 (m-80) REVERT: A 543 LYS cc_start: 0.7711 (tppt) cc_final: 0.7400 (ttmm) REVERT: A 577 ASP cc_start: 0.9258 (t0) cc_final: 0.9046 (t0) REVERT: A 689 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8392 (mm-30) REVERT: F 190 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8800 (mttp) REVERT: F 449 MET cc_start: 0.8358 (tpp) cc_final: 0.7997 (tpp) REVERT: F 487 ARG cc_start: 0.8890 (ttp-110) cc_final: 0.8551 (mtp-110) REVERT: F 603 GLN cc_start: 0.8066 (mt0) cc_final: 0.7590 (mt0) REVERT: E 230 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7958 (t80) REVERT: E 491 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8125 (tt0) REVERT: E 564 ASP cc_start: 0.9042 (m-30) cc_final: 0.8469 (m-30) REVERT: E 567 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8443 (ttm-80) REVERT: E 625 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7647 (mmp-170) REVERT: E 700 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7351 (ttp80) REVERT: E 740 MET cc_start: 0.8582 (tpt) cc_final: 0.8333 (tpt) REVERT: E 756 GLU cc_start: 0.8551 (tp30) cc_final: 0.7901 (pp20) REVERT: E 757 MET cc_start: 0.7665 (ppp) cc_final: 0.6068 (ptp) REVERT: D 52 PHE cc_start: 0.7869 (m-80) cc_final: 0.6271 (t80) REVERT: D 74 ASP cc_start: 0.7881 (t0) cc_final: 0.7419 (t0) REVERT: D 322 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6766 (ptt-90) REVERT: D 383 ILE cc_start: 0.9478 (mt) cc_final: 0.9209 (mt) REVERT: D 426 LYS cc_start: 0.7858 (tptt) cc_final: 0.7639 (tptt) REVERT: D 427 MET cc_start: 0.4416 (tpt) cc_final: 0.3381 (tpt) REVERT: D 577 ASP cc_start: 0.8433 (t0) cc_final: 0.8029 (t0) REVERT: D 630 ASP cc_start: 0.8019 (t70) cc_final: 0.7215 (t0) REVERT: G 159 MET cc_start: -0.0768 (ttm) cc_final: -0.1110 (mmm) REVERT: G 393 LEU cc_start: 0.6462 (mt) cc_final: 0.6260 (mm) outliers start: 113 outliers final: 89 residues processed: 625 average time/residue: 0.2163 time to fit residues: 220.7504 Evaluate side-chains 607 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 513 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 625 ARG Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 315 optimal weight: 0.8980 chunk 487 optimal weight: 0.6980 chunk 103 optimal weight: 0.0570 chunk 360 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN B 490 GLN F 443 ASN F 750 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.155537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110588 restraints weight = 72523.953| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.27 r_work: 0.3357 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 40235 Z= 0.123 Angle : 0.637 15.161 54400 Z= 0.304 Chirality : 0.044 0.240 6133 Planarity : 0.005 0.083 7130 Dihedral : 7.175 158.197 5554 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.44 % Allowed : 16.07 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.12), residues: 4965 helix: 1.34 (0.11), residues: 2276 sheet: 0.27 (0.18), residues: 846 loop : 0.52 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 453 TYR 0.026 0.002 TYR E 517 PHE 0.019 0.001 PHE D 742 TRP 0.030 0.001 TRP C 476 HIS 0.014 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00282 (40235) covalent geometry : angle 0.63686 (54400) hydrogen bonds : bond 0.03543 ( 1863) hydrogen bonds : angle 4.25213 ( 5226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 548 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.7262 (pt0) cc_final: 0.6472 (mm-30) REVERT: C 123 VAL cc_start: 0.7721 (t) cc_final: 0.7475 (p) REVERT: C 162 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 309 ILE cc_start: 0.8599 (tt) cc_final: 0.8262 (tt) REVERT: C 426 LYS cc_start: 0.8474 (tttt) cc_final: 0.8122 (mtmm) REVERT: C 464 LEU cc_start: 0.9064 (tp) cc_final: 0.8536 (mt) REVERT: B 75 ASP cc_start: 0.7208 (t0) cc_final: 0.6765 (t0) REVERT: B 229 LEU cc_start: 0.7939 (mm) cc_final: 0.6885 (tp) REVERT: B 352 SER cc_start: 0.8658 (m) cc_final: 0.8247 (t) REVERT: B 529 LYS cc_start: 0.8718 (mttt) cc_final: 0.8492 (mtpt) REVERT: B 578 GLU cc_start: 0.8184 (tp30) cc_final: 0.7759 (tp30) REVERT: B 608 MET cc_start: 0.8292 (mtm) cc_final: 0.7436 (mtm) REVERT: H 64 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6470 (tp30) REVERT: H 159 MET cc_start: 0.1009 (mmm) cc_final: 0.0381 (tpt) REVERT: H 354 TYR cc_start: 0.7529 (m-80) cc_final: 0.6342 (m-80) REVERT: H 363 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6673 (t80) REVERT: H 407 THR cc_start: 0.7507 (m) cc_final: 0.6839 (t) REVERT: A 35 ASP cc_start: 0.8632 (t0) cc_final: 0.8104 (t70) REVERT: A 63 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8417 (mttm) REVERT: A 150 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: A 315 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8594 (mmtm) REVERT: A 352 SER cc_start: 0.9246 (m) cc_final: 0.8786 (t) REVERT: A 466 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: A 483 GLU cc_start: 0.8578 (pm20) cc_final: 0.7965 (pt0) REVERT: A 543 LYS cc_start: 0.7726 (tppt) cc_final: 0.7430 (ttmm) REVERT: A 577 ASP cc_start: 0.9233 (t0) cc_final: 0.9015 (t0) REVERT: A 618 PHE cc_start: 0.8269 (t80) cc_final: 0.7803 (t80) REVERT: A 689 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8389 (mm-30) REVERT: F 52 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6585 (t80) REVERT: F 190 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8829 (mttp) REVERT: F 332 MET cc_start: 0.8494 (tpp) cc_final: 0.8190 (mtt) REVERT: F 487 ARG cc_start: 0.8872 (ttp-110) cc_final: 0.8532 (mtp-110) REVERT: F 598 ASP cc_start: 0.7366 (t0) cc_final: 0.6772 (t0) REVERT: F 599 ARG cc_start: 0.8586 (mpp80) cc_final: 0.7978 (mpp80) REVERT: F 603 GLN cc_start: 0.8078 (mt0) cc_final: 0.7681 (mt0) REVERT: E 115 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7634 (t70) REVERT: E 230 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8240 (t80) REVERT: E 564 ASP cc_start: 0.9018 (m-30) cc_final: 0.8465 (m-30) REVERT: E 567 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8421 (ttm-80) REVERT: E 625 ARG cc_start: 0.8139 (tpp-160) cc_final: 0.7700 (mmp-170) REVERT: E 700 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7379 (ttp80) REVERT: E 756 GLU cc_start: 0.8545 (tp30) cc_final: 0.7605 (pt0) REVERT: E 757 MET cc_start: 0.7606 (ppp) cc_final: 0.6777 (ptp) REVERT: D 52 PHE cc_start: 0.7847 (m-80) cc_final: 0.6400 (t80) REVERT: D 74 ASP cc_start: 0.7903 (t0) cc_final: 0.7430 (t0) REVERT: D 322 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6780 (ptt-90) REVERT: D 383 ILE cc_start: 0.9418 (mt) cc_final: 0.9155 (mt) REVERT: D 426 LYS cc_start: 0.7831 (tptt) cc_final: 0.7611 (tptp) REVERT: D 427 MET cc_start: 0.4357 (tpt) cc_final: 0.3323 (tpt) REVERT: D 564 ASP cc_start: 0.8696 (m-30) cc_final: 0.8382 (m-30) REVERT: D 577 ASP cc_start: 0.8433 (t0) cc_final: 0.8029 (t0) REVERT: D 630 ASP cc_start: 0.8035 (t70) cc_final: 0.7177 (t0) REVERT: G 159 MET cc_start: -0.0770 (ttm) cc_final: -0.1122 (mmm) outliers start: 104 outliers final: 86 residues processed: 618 average time/residue: 0.2146 time to fit residues: 217.9414 Evaluate side-chains 612 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 520 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 625 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 757 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 208 optimal weight: 0.2980 chunk 269 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 255 optimal weight: 1.9990 chunk 442 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 487 optimal weight: 0.4980 chunk 491 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 494 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN F 750 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118994 restraints weight = 72258.040| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.21 r_work: 0.3369 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 40235 Z= 0.111 Angle : 0.638 14.210 54400 Z= 0.301 Chirality : 0.044 0.235 6133 Planarity : 0.005 0.082 7130 Dihedral : 6.687 144.108 5554 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.09 % Allowed : 16.47 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.12), residues: 4965 helix: 1.41 (0.11), residues: 2274 sheet: 0.36 (0.18), residues: 841 loop : 0.58 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 453 TYR 0.028 0.001 TYR A 244 PHE 0.021 0.001 PHE D 742 TRP 0.033 0.001 TRP C 476 HIS 0.015 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00252 (40235) covalent geometry : angle 0.63838 (54400) hydrogen bonds : bond 0.03368 ( 1863) hydrogen bonds : angle 4.21000 ( 5226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 559 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.7208 (pt0) cc_final: 0.6135 (tm-30) REVERT: C 123 VAL cc_start: 0.7697 (t) cc_final: 0.7444 (p) REVERT: C 162 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7045 (mt-10) REVERT: C 309 ILE cc_start: 0.8537 (tt) cc_final: 0.8191 (tt) REVERT: C 426 LYS cc_start: 0.8423 (tttt) cc_final: 0.8058 (mtmm) REVERT: C 464 LEU cc_start: 0.9006 (tp) cc_final: 0.8585 (mt) REVERT: B 75 ASP cc_start: 0.7153 (t0) cc_final: 0.6663 (t0) REVERT: B 229 LEU cc_start: 0.7884 (mm) cc_final: 0.7404 (mt) REVERT: B 317 HIS cc_start: 0.5344 (OUTLIER) cc_final: 0.3900 (p-80) REVERT: B 352 SER cc_start: 0.8589 (m) cc_final: 0.8163 (t) REVERT: B 529 LYS cc_start: 0.8645 (mttt) cc_final: 0.8437 (mtpt) REVERT: B 578 GLU cc_start: 0.8139 (tp30) cc_final: 0.7720 (tp30) REVERT: B 608 MET cc_start: 0.8207 (mtm) cc_final: 0.7407 (mtm) REVERT: H 159 MET cc_start: 0.0997 (mmm) cc_final: 0.0378 (tpt) REVERT: H 354 TYR cc_start: 0.7465 (m-80) cc_final: 0.6681 (m-80) REVERT: H 363 TYR cc_start: 0.6947 (m-80) cc_final: 0.6645 (t80) REVERT: H 407 THR cc_start: 0.7494 (m) cc_final: 0.6817 (t) REVERT: A 35 ASP cc_start: 0.8662 (t0) cc_final: 0.8107 (t70) REVERT: A 63 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8434 (mttm) REVERT: A 150 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: A 315 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8557 (mmtm) REVERT: A 352 SER cc_start: 0.9260 (m) cc_final: 0.8799 (t) REVERT: A 438 ASP cc_start: 0.8664 (t0) cc_final: 0.8169 (t70) REVERT: A 466 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: A 483 GLU cc_start: 0.8605 (pm20) cc_final: 0.8073 (pt0) REVERT: A 487 ARG cc_start: 0.8387 (ptp-110) cc_final: 0.7485 (mmm160) REVERT: A 543 LYS cc_start: 0.7726 (tppt) cc_final: 0.7437 (ttmm) REVERT: A 577 ASP cc_start: 0.9232 (t0) cc_final: 0.9021 (t0) REVERT: A 618 PHE cc_start: 0.8299 (t80) cc_final: 0.7742 (t80) REVERT: A 689 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8483 (mm-30) REVERT: F 52 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6699 (t80) REVERT: F 236 LYS cc_start: 0.7397 (tptt) cc_final: 0.6970 (ttpp) REVERT: F 332 MET cc_start: 0.8408 (tpp) cc_final: 0.8159 (mtt) REVERT: F 366 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8298 (mt-10) REVERT: F 430 ILE cc_start: 0.5996 (mt) cc_final: 0.5687 (mt) REVERT: F 487 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8541 (mtp-110) REVERT: F 599 ARG cc_start: 0.8663 (mpp80) cc_final: 0.8018 (mpp80) REVERT: F 603 GLN cc_start: 0.8058 (mt0) cc_final: 0.7694 (mt0) REVERT: E 30 GLU cc_start: 0.8633 (tt0) cc_final: 0.8363 (tt0) REVERT: E 115 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7669 (t70) REVERT: E 230 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8070 (t80) REVERT: E 332 MET cc_start: 0.8920 (mmm) cc_final: 0.8678 (mmp) REVERT: E 564 ASP cc_start: 0.9033 (m-30) cc_final: 0.8463 (m-30) REVERT: E 567 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8394 (ttm-80) REVERT: E 625 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7706 (mmp-170) REVERT: E 700 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7398 (ttp80) REVERT: E 732 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6819 (mtm110) REVERT: E 756 GLU cc_start: 0.8536 (tp30) cc_final: 0.7650 (pt0) REVERT: D 52 PHE cc_start: 0.7878 (m-80) cc_final: 0.6436 (t80) REVERT: D 74 ASP cc_start: 0.7862 (t0) cc_final: 0.7417 (t0) REVERT: D 144 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7754 (mtt-85) REVERT: D 322 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6758 (ptt-90) REVERT: D 383 ILE cc_start: 0.9347 (mt) cc_final: 0.9101 (mt) REVERT: D 427 MET cc_start: 0.4354 (tpt) cc_final: 0.3340 (tpt) REVERT: D 564 ASP cc_start: 0.8698 (m-30) cc_final: 0.8376 (m-30) REVERT: D 577 ASP cc_start: 0.8395 (t0) cc_final: 0.7959 (t0) REVERT: D 756 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: G 159 MET cc_start: -0.0796 (ttm) cc_final: -0.1138 (mmm) REVERT: G 393 LEU cc_start: 0.6150 (mm) cc_final: 0.5940 (mt) outliers start: 89 outliers final: 70 residues processed: 621 average time/residue: 0.2062 time to fit residues: 210.5713 Evaluate side-chains 606 residues out of total 4256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 528 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 757 MET Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 167 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 416 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 458 optimal weight: 0.0970 chunk 296 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 457 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 499 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 750 ASN F 763 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.156477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111899 restraints weight = 72696.507| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.28 r_work: 0.3373 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40235 Z= 0.119 Angle : 0.638 14.111 54400 Z= 0.300 Chirality : 0.044 0.230 6133 Planarity : 0.004 0.081 7130 Dihedral : 6.401 132.968 5554 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.11 % Allowed : 16.64 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.12), residues: 4965 helix: 1.45 (0.11), residues: 2273 sheet: 0.38 (0.18), residues: 841 loop : 0.58 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 560 TYR 0.027 0.002 TYR E 517 PHE 0.019 0.001 PHE D 742 TRP 0.011 0.001 TRP E 551 HIS 0.016 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00275 (40235) covalent geometry : angle 0.63798 (54400) hydrogen bonds : bond 0.03367 ( 1863) hydrogen bonds : angle 4.20420 ( 5226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11214.29 seconds wall clock time: 191 minutes 45.63 seconds (11505.63 seconds total)