Starting phenix.real_space_refine on Tue Aug 26 17:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcp_28989/08_2025/8fcp_28989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcp_28989/08_2025/8fcp_28989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fcp_28989/08_2025/8fcp_28989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcp_28989/08_2025/8fcp_28989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcp_28989/08_2025/8fcp_28989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcp_28989/08_2025/8fcp_28989.map" } resolution = 3.52 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= 0.056 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 196 5.16 5 C 24794 2.51 5 N 6932 2.21 5 O 7548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.04s 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: 39494 Number of models: 1 Model: "" Number of chains: 14 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: "C" 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: "B" 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: "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: 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: "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: "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} 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} Time building chain proxies: 10.46, per 1000 atoms: 0.26 Number of scatterers: 39494 At special positions: 0 Unit cell: (195.99, 181.812, 118.428, 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 196 16.00 P 24 15.00 O 7548 8.00 N 6932 7.00 C 24794 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: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 476.8 nanoseconds 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9352 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 42 sheets defined 52.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.485A 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: 4.011A 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: 3.836A 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 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 427 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: 3.508A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.227A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.703A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.503A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 removed outlier: 3.504A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 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: 4.812A 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: 3.929A 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 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 427 Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 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 removed outlier: 3.695A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.608A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.577A 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 705 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.508A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) 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: 5.018A 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 227 through 232 removed outlier: 3.859A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (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 removed outlier: 3.509A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) 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 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 349 through 353 removed outlier: 4.105A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 4.456A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) 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 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.936A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 610 through 611 No H-bonds generated for 'chain 'C' and resid 610 through 611' Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.909A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 707 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' 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: 3.776A pdb=" N PHE H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 165 removed outlier: 4.103A pdb=" N ASN H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 188 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 280 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: 3.920A pdb=" N VAL H 362 " --> pdb=" O ARG H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 421 removed outlier: 3.552A 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 'B' and resid 42 through 49 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 139 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.605A 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 226 through 233 removed outlier: 4.001A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) 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: 3.506A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.803A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 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 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 428 removed outlier: 3.760A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (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 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.518A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.185A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.552A 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 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.509A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 3.525A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) 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: 4.785A 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: 3.947A 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 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: 3.702A 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: 3.598A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.717A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 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 50 removed outlier: 3.558A 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 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: 5.056A 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 removed outlier: 4.064A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) 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: 3.511A 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: 3.501A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (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: 4.137A 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: 4.351A 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 Proline residue: F 496 - end of helix 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: 3.963A 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: 3.656A 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 Processing helix chain 'F' and resid 748 through 763 Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.779A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 164 Processing helix chain 'G' and resid 167 through 188 removed outlier: 3.523A pdb=" N ILE G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) 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 250 through 262 Processing helix chain 'G' and resid 280 through 285 Processing helix chain 'G' and resid 296 through 316 Processing helix chain 'G' and resid 319 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.927A pdb=" N VAL G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 399 Processing helix chain 'G' and resid 411 through 421 removed outlier: 3.531A 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 'E' and resid 25 through 30 removed outlier: 7.881A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.637A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.157A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.375A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.268A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.550A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.770A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.045A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.467A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 29 Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.642A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.818A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.391A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.535A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 131 through 133 Processing sheet with id=AC2, first strand: chain 'H' and resid 196 through 198 Processing sheet with id=AC3, first strand: chain 'H' and resid 386 through 387 removed outlier: 4.615A pdb=" N LEU H 379 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ALA H 404 " --> pdb=" O TYR H 336 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU H 338 " --> pdb=" O ALA H 404 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU H 406 " --> pdb=" O LEU H 338 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG H 340 " --> pdb=" O LEU H 406 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE H 408 " --> pdb=" O ARG H 340 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG H 342 " --> pdb=" O PHE H 408 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N TRP H 410 " --> pdb=" O ARG H 342 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.834A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.668A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AC7, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AC8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.134A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.365A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.277A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.481A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AD4, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.768A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.049A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.455A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 25 through 29 Processing sheet with id=AD8, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.661A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AE1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AE2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.383A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.542A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (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: 4.595A pdb=" N LEU G 379 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU G 338 " --> pdb=" O ALA G 404 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU G 406 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG G 340 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE G 408 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 342 " --> pdb=" O PHE G 408 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N TRP G 410 " --> pdb=" O ARG G 342 " (cutoff:3.500A) 1857 hydrogen bonds defined for protein. 5220 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: 10.61 Time building geometry restraints manager: 4.66 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: 8161 1.33 - 1.45: 8377 1.45 - 1.57: 23272 1.57 - 1.69: 36 1.69 - 1.81: 310 Bond restraints: 40156 Sorted by residual: bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+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 3.05e+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 3.03e+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 3.01e+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 3.01e+01 ... (remaining 40151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 53021 2.49 - 4.98: 1123 4.98 - 7.47: 107 7.47 - 9.96: 33 9.96 - 12.45: 10 Bond angle restraints: 54294 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 113.28 124.02 -10.74 1.22e+00 6.72e-01 7.75e+01 angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.28 123.94 -10.66 1.22e+00 6.72e-01 7.64e+01 angle pdb=" N ARG H 332 " pdb=" CA ARG H 332 " pdb=" C ARG H 332 " ideal model delta sigma weight residual 112.88 122.46 -9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 112.88 122.44 -9.56 1.29e+00 6.01e-01 5.49e+01 angle pdb=" CA ASP C 592 " pdb=" C ASP C 592 " pdb=" O ASP C 592 " ideal model delta sigma weight residual 117.94 121.75 -3.81 5.80e-01 2.97e+00 4.31e+01 ... (remaining 54289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 24523 34.01 - 68.01: 284 68.01 - 102.02: 37 102.02 - 136.02: 12 136.02 - 170.03: 10 Dihedral angle restraints: 24866 sinusoidal: 10458 harmonic: 14408 Sorted by residual: dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 129.97 170.03 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual 300.00 132.03 167.97 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 143.74 156.26 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 24863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4352 0.047 - 0.094: 1069 0.094 - 0.141: 480 0.141 - 0.189: 211 0.189 - 0.236: 12 Chirality restraints: 6124 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 1.39e+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 chirality pdb=" CA ILE F 590 " pdb=" N ILE F 590 " pdb=" C ILE F 590 " pdb=" CB ILE F 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 6121 not shown) Planarity restraints: 7116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 254 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C GLU H 254 " -0.040 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 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+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 F 534 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.26e+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 ... (remaining 7113 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 14488 2.89 - 3.39: 38102 3.39 - 3.90: 67249 3.90 - 4.40: 76974 4.40 - 4.90: 125045 Nonbonded interactions: 321858 Sorted by model distance: nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.390 3.120 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.391 3.120 nonbonded pdb=" NZ LYS C 211 " pdb=" O ALA C 570 " model vdw 2.416 3.120 nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.434 3.120 nonbonded pdb=" OD2 ASP H 176 " pdb=" NZ LYS H 180 " model vdw 2.438 3.120 ... (remaining 321853 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 902)) selection = chain 'C' 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.170 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: 0.060 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 40.510 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 0.111 40156 Z= 0.623 Angle : 0.891 12.445 54294 Z= 0.563 Chirality : 0.058 0.236 6124 Planarity : 0.004 0.032 7116 Dihedral : 12.106 170.027 15514 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.76 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 0.54 (0.11), residues: 4954 helix: 0.03 (0.10), residues: 2180 sheet: 0.60 (0.16), residues: 858 loop : 0.97 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 653 TYR 0.001 0.000 TYR G 363 PHE 0.002 0.000 PHE A 266 TRP 0.002 0.000 TRP B 454 HIS 0.001 0.000 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.01090 (40156) covalent geometry : angle 0.89102 (54294) hydrogen bonds : bond 0.20769 ( 1857) hydrogen bonds : angle 6.36004 ( 5220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1400 time to evaluate : 1.639 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 LEU cc_start: 0.5774 (mt) cc_final: 0.5477 (mt) REVERT: D 441 VAL cc_start: 0.7972 (t) cc_final: 0.7676 (p) REVERT: C 102 ILE cc_start: 0.8732 (mp) cc_final: 0.8186 (mt) REVERT: C 332 MET cc_start: 0.7129 (mmm) cc_final: 0.6896 (mmm) REVERT: B 138 TYR cc_start: 0.7031 (t80) cc_final: 0.6822 (t80) REVERT: B 449 MET cc_start: 0.7805 (tpt) cc_final: 0.7580 (tpp) REVERT: A 26 LEU cc_start: 0.5629 (mt) cc_final: 0.5311 (mt) REVERT: A 182 ILE cc_start: 0.7834 (mt) cc_final: 0.7620 (mt) REVERT: A 420 LEU cc_start: 0.7519 (tp) cc_final: 0.7309 (tp) REVERT: A 441 VAL cc_start: 0.8280 (t) cc_final: 0.6758 (t) REVERT: F 102 ILE cc_start: 0.8919 (mt) cc_final: 0.8521 (mt) outliers start: 0 outliers final: 0 residues processed: 1400 average time/residue: 0.2901 time to fit residues: 625.4300 Evaluate side-chains 687 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 494 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 641 GLN D 660 ASN C 115 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS C 603 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 499 HIS A 348 ASN A 641 GLN A 660 ASN F 115 HIS ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN G 278 GLN G 294 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.169137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130721 restraints weight = 75946.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132141 restraints weight = 44672.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132739 restraints weight = 31605.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133374 restraints weight = 28341.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133486 restraints weight = 25559.689| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40156 Z= 0.154 Angle : 0.679 10.504 54294 Z= 0.340 Chirality : 0.046 0.216 6124 Planarity : 0.005 0.067 7116 Dihedral : 9.903 167.850 5544 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.33 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 10.17 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.45 (0.12), residues: 4954 helix: 1.14 (0.11), residues: 2250 sheet: 0.81 (0.17), residues: 826 loop : 1.09 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 313 TYR 0.025 0.002 TYR A 755 PHE 0.024 0.002 PHE C 52 TRP 0.013 0.002 TRP H 374 HIS 0.008 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00341 (40156) covalent geometry : angle 0.67897 (54294) hydrogen bonds : bond 0.05382 ( 1857) hydrogen bonds : angle 4.60000 ( 5220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 734 time to evaluate : 1.620 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 ASN cc_start: 0.7449 (t0) cc_final: 0.7147 (t0) REVERT: E 138 TYR cc_start: 0.7739 (t80) cc_final: 0.7519 (t80) REVERT: E 158 MET cc_start: 0.8183 (mmm) cc_final: 0.7812 (mmt) REVERT: E 393 ASP cc_start: 0.7911 (t0) cc_final: 0.7671 (t0) REVERT: D 26 LEU cc_start: 0.7408 (mt) cc_final: 0.6819 (mt) REVERT: D 72 LEU cc_start: 0.8397 (tp) cc_final: 0.7850 (tt) REVERT: D 135 LEU cc_start: 0.8519 (tp) cc_final: 0.8129 (tt) REVERT: D 183 HIS cc_start: 0.6044 (t70) cc_final: 0.5661 (t-170) REVERT: D 508 MET cc_start: 0.7287 (tpt) cc_final: 0.6915 (tpt) REVERT: D 678 MET cc_start: 0.8316 (mmm) cc_final: 0.8041 (mmm) REVERT: C 332 MET cc_start: 0.8163 (mmm) cc_final: 0.7890 (mmm) REVERT: C 757 MET cc_start: 0.7251 (tpp) cc_final: 0.7010 (tpp) REVERT: H 338 LEU cc_start: 0.7451 (mm) cc_final: 0.6725 (tt) REVERT: B 129 ASN cc_start: 0.7585 (t0) cc_final: 0.7313 (t0) REVERT: B 506 PHE cc_start: 0.8271 (m-80) cc_final: 0.8024 (m-10) REVERT: B 742 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6794 (t80) REVERT: A 72 LEU cc_start: 0.8391 (tp) cc_final: 0.7776 (tt) REVERT: A 182 ILE cc_start: 0.8386 (mt) cc_final: 0.8179 (mt) REVERT: A 183 HIS cc_start: 0.6002 (t70) cc_final: 0.5642 (t-170) REVERT: A 678 MET cc_start: 0.8358 (mmm) cc_final: 0.8048 (mmm) REVERT: F 332 MET cc_start: 0.8047 (mmm) cc_final: 0.7796 (mmm) REVERT: F 546 GLU cc_start: 0.7982 (tp30) cc_final: 0.7409 (tm-30) outliers start: 86 outliers final: 50 residues processed: 787 average time/residue: 0.2578 time to fit residues: 328.9918 Evaluate side-chains 600 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 549 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 452 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 400 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 490 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 187 optimal weight: 0.4980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 327 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS C 558 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 443 ASN B 602 ASN B 603 GLN A 660 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 327 GLN F 443 ASN F 603 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.161870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123664 restraints weight = 74742.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122389 restraints weight = 49282.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123910 restraints weight = 36322.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124163 restraints weight = 32079.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124651 restraints weight = 27682.276| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 40156 Z= 0.250 Angle : 0.738 10.993 54294 Z= 0.365 Chirality : 0.048 0.182 6124 Planarity : 0.005 0.057 7116 Dihedral : 9.588 167.575 5544 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.04 % Allowed : 11.65 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.26 (0.12), residues: 4954 helix: 1.16 (0.11), residues: 2250 sheet: 0.65 (0.17), residues: 838 loop : 0.75 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 340 TYR 0.032 0.002 TYR C 244 PHE 0.026 0.002 PHE B 674 TRP 0.015 0.002 TRP G 374 HIS 0.006 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00582 (40156) covalent geometry : angle 0.73844 (54294) hydrogen bonds : bond 0.04743 ( 1857) hydrogen bonds : angle 4.57953 ( 5220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 592 time to evaluate : 1.676 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: E 129 ASN cc_start: 0.7758 (t0) cc_final: 0.7450 (t0) REVERT: E 158 MET cc_start: 0.8382 (mmm) cc_final: 0.8092 (mmt) REVERT: E 435 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7100 (tm-30) REVERT: E 745 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7291 (ptm-80) REVERT: D 135 LEU cc_start: 0.8578 (tp) cc_final: 0.8280 (tt) REVERT: D 183 HIS cc_start: 0.6134 (t70) cc_final: 0.5824 (t70) REVERT: C 603 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: C 607 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8812 (mm-30) REVERT: C 757 MET cc_start: 0.7523 (tpp) cc_final: 0.7279 (tpp) REVERT: H 338 LEU cc_start: 0.7452 (mm) cc_final: 0.6684 (tt) REVERT: B 98 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8511 (m-30) REVERT: B 129 ASN cc_start: 0.7819 (t0) cc_final: 0.7579 (t0) REVERT: B 435 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7117 (tt0) REVERT: B 603 GLN cc_start: 0.8971 (mm110) cc_final: 0.8641 (mp10) REVERT: B 742 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6933 (t80) REVERT: B 745 ARG cc_start: 0.7777 (ptm160) cc_final: 0.7292 (ptm-80) REVERT: A 183 HIS cc_start: 0.6196 (t70) cc_final: 0.5821 (t-90) REVERT: A 203 TYR cc_start: 0.9094 (m-80) cc_final: 0.8860 (m-80) REVERT: A 508 MET cc_start: 0.7480 (tpp) cc_final: 0.7277 (ttt) REVERT: A 580 ASP cc_start: 0.7942 (p0) cc_final: 0.7668 (p0) REVERT: F 217 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8779 (mtmm) REVERT: F 560 ARG cc_start: 0.8280 (mtp85) cc_final: 0.8060 (mtp85) outliers start: 129 outliers final: 88 residues processed: 684 average time/residue: 0.2506 time to fit residues: 282.4905 Evaluate side-chains 583 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 491 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 241 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 361 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 457 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 395 optimal weight: 0.4980 chunk 76 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 603 GLN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 660 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.163430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125837 restraints weight = 75108.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125368 restraints weight = 49091.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127000 restraints weight = 34524.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127208 restraints weight = 30663.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127478 restraints weight = 27085.697| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40156 Z= 0.131 Angle : 0.623 8.905 54294 Z= 0.305 Chirality : 0.045 0.200 6124 Planarity : 0.004 0.055 7116 Dihedral : 9.122 141.983 5544 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.52 % Allowed : 13.14 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.43 (0.12), residues: 4954 helix: 1.42 (0.11), residues: 2244 sheet: 0.62 (0.17), residues: 844 loop : 0.74 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 560 TYR 0.023 0.002 TYR C 244 PHE 0.024 0.001 PHE B 576 TRP 0.013 0.001 TRP H 374 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00295 (40156) covalent geometry : angle 0.62278 (54294) hydrogen bonds : bond 0.03928 ( 1857) hydrogen bonds : angle 4.27615 ( 5220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 570 time to evaluate : 1.683 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: E 129 ASN cc_start: 0.7766 (t0) cc_final: 0.7498 (t0) REVERT: E 158 MET cc_start: 0.8301 (mmm) cc_final: 0.8043 (mmt) REVERT: E 435 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7179 (tm-30) REVERT: E 466 GLU cc_start: 0.7576 (tp30) cc_final: 0.7257 (tp30) REVERT: E 467 THR cc_start: 0.8756 (m) cc_final: 0.8434 (t) REVERT: E 603 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8810 (mp10) REVERT: E 745 ARG cc_start: 0.7690 (ptm160) cc_final: 0.7097 (ptm-80) REVERT: D 135 LEU cc_start: 0.8495 (tp) cc_final: 0.8213 (tp) REVERT: D 183 HIS cc_start: 0.6269 (t70) cc_final: 0.5928 (t70) REVERT: D 397 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 427 MET cc_start: 0.8243 (tmm) cc_final: 0.7784 (tpp) REVERT: D 603 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8039 (tp-100) REVERT: C 217 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8828 (mtmm) REVERT: C 218 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8783 (tm-30) REVERT: C 230 PHE cc_start: 0.7094 (m-80) cc_final: 0.6882 (m-80) REVERT: C 757 MET cc_start: 0.7614 (tpp) cc_final: 0.7334 (tpp) REVERT: H 338 LEU cc_start: 0.7526 (mm) cc_final: 0.6818 (tt) REVERT: B 133 VAL cc_start: 0.8451 (m) cc_final: 0.8112 (p) REVERT: B 315 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7574 (tptt) REVERT: B 435 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7167 (tt0) REVERT: B 508 MET cc_start: 0.7565 (tpt) cc_final: 0.7083 (tpt) REVERT: B 578 GLU cc_start: 0.7758 (tt0) cc_final: 0.7327 (tt0) REVERT: B 603 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8704 (mp10) REVERT: B 742 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6863 (t80) REVERT: B 745 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7108 (ptm-80) REVERT: A 147 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6824 (ttm-80) REVERT: A 183 HIS cc_start: 0.6153 (t70) cc_final: 0.5812 (t70) REVERT: A 203 TYR cc_start: 0.9115 (m-80) cc_final: 0.8886 (m-80) REVERT: A 492 LEU cc_start: 0.8806 (mm) cc_final: 0.8472 (mt) REVERT: A 580 ASP cc_start: 0.8014 (p0) cc_final: 0.7813 (p0) REVERT: F 217 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8825 (mtmm) REVERT: F 218 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8779 (tm-30) REVERT: G 338 LEU cc_start: 0.7368 (mm) cc_final: 0.6702 (tt) REVERT: G 356 ARG cc_start: 0.5532 (ptt180) cc_final: 0.5273 (ptt-90) outliers start: 107 outliers final: 76 residues processed: 636 average time/residue: 0.2391 time to fit residues: 254.1533 Evaluate side-chains 571 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 491 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 391 optimal weight: 0.9990 chunk 469 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 229 optimal weight: 30.0000 chunk 136 optimal weight: 0.8980 chunk 435 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 chunk 385 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 HIS E 337 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.161036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124488 restraints weight = 75327.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123134 restraints weight = 46906.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124416 restraints weight = 35538.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125009 restraints weight = 29421.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125285 restraints weight = 26548.772| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40156 Z= 0.163 Angle : 0.628 9.254 54294 Z= 0.306 Chirality : 0.045 0.210 6124 Planarity : 0.004 0.055 7116 Dihedral : 8.654 136.244 5544 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.92 % Allowed : 13.54 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.43 (0.12), residues: 4954 helix: 1.48 (0.11), residues: 2250 sheet: 0.62 (0.17), residues: 824 loop : 0.63 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 625 TYR 0.021 0.002 TYR C 244 PHE 0.023 0.001 PHE A 152 TRP 0.016 0.002 TRP C 551 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00382 (40156) covalent geometry : angle 0.62756 (54294) hydrogen bonds : bond 0.03801 ( 1857) hydrogen bonds : angle 4.24373 ( 5220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 541 time to evaluate : 1.384 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: E 129 ASN cc_start: 0.7740 (t0) cc_final: 0.7509 (t0) REVERT: E 158 MET cc_start: 0.8278 (mmm) cc_final: 0.8042 (mmt) REVERT: E 435 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7419 (tm-30) REVERT: E 467 THR cc_start: 0.8813 (m) cc_final: 0.8525 (m) REVERT: E 603 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8774 (mp10) REVERT: E 745 ARG cc_start: 0.7723 (ptm160) cc_final: 0.7081 (ptm-80) REVERT: D 135 LEU cc_start: 0.8426 (tp) cc_final: 0.8135 (tp) REVERT: D 183 HIS cc_start: 0.6386 (t70) cc_final: 0.6028 (t70) REVERT: D 244 TYR cc_start: 0.7963 (p90) cc_final: 0.7675 (p90) REVERT: D 397 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8330 (tm-30) REVERT: D 427 MET cc_start: 0.8328 (tmm) cc_final: 0.7932 (tmm) REVERT: D 435 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7098 (mm-30) REVERT: D 492 LEU cc_start: 0.8640 (mm) cc_final: 0.8304 (mt) REVERT: D 543 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7998 (mtpt) REVERT: D 603 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8139 (tp-100) REVERT: C 217 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8824 (mtmm) REVERT: C 607 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8732 (mm-30) REVERT: C 757 MET cc_start: 0.7609 (tpp) cc_final: 0.7348 (tpp) REVERT: H 338 LEU cc_start: 0.7564 (mm) cc_final: 0.6786 (tt) REVERT: B 123 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8457 (m) REVERT: B 321 GLU cc_start: 0.7694 (mp0) cc_final: 0.7401 (mt-10) REVERT: B 435 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7598 (pm20) REVERT: B 560 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7851 (mtm180) REVERT: B 563 PHE cc_start: 0.9159 (m-80) cc_final: 0.8948 (m-80) REVERT: B 578 GLU cc_start: 0.8008 (tt0) cc_final: 0.7621 (tt0) REVERT: B 603 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8742 (mp10) REVERT: B 742 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6786 (t80) REVERT: B 745 ARG cc_start: 0.7728 (ptm160) cc_final: 0.7090 (ptm-80) REVERT: A 147 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6735 (ttm-80) REVERT: A 183 HIS cc_start: 0.6217 (t70) cc_final: 0.5860 (t70) REVERT: A 492 LEU cc_start: 0.8781 (mm) cc_final: 0.8472 (mt) REVERT: A 580 ASP cc_start: 0.8074 (p0) cc_final: 0.7861 (p0) REVERT: F 140 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7830 (tt) REVERT: F 217 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8828 (mtmm) REVERT: F 218 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8822 (tm-30) REVERT: F 546 GLU cc_start: 0.8250 (tp30) cc_final: 0.7986 (tp30) REVERT: G 338 LEU cc_start: 0.7504 (mm) cc_final: 0.6825 (tt) REVERT: G 356 ARG cc_start: 0.5714 (ptt180) cc_final: 0.5488 (ptt-90) outliers start: 124 outliers final: 89 residues processed: 625 average time/residue: 0.2265 time to fit residues: 233.7187 Evaluate side-chains 575 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 478 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 736 PHE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 434 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 48 optimal weight: 8.9990 chunk 438 optimal weight: 5.9990 chunk 489 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 470 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 337 GLN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.154549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116860 restraints weight = 76062.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115404 restraints weight = 50389.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116349 restraints weight = 36021.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117126 restraints weight = 30385.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117195 restraints weight = 26691.776| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 40156 Z= 0.260 Angle : 0.725 9.532 54294 Z= 0.356 Chirality : 0.048 0.246 6124 Planarity : 0.005 0.091 7116 Dihedral : 8.514 134.102 5544 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.39 % Allowed : 14.29 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.11 (0.12), residues: 4954 helix: 1.28 (0.11), residues: 2240 sheet: 0.41 (0.18), residues: 798 loop : 0.41 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 625 TYR 0.027 0.002 TYR D 203 PHE 0.020 0.002 PHE G 377 TRP 0.018 0.002 TRP C 551 HIS 0.006 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00612 (40156) covalent geometry : angle 0.72540 (54294) hydrogen bonds : bond 0.04230 ( 1857) hydrogen bonds : angle 4.49741 ( 5220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 516 time to evaluate : 1.380 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: E 129 ASN cc_start: 0.7764 (t0) cc_final: 0.7546 (t0) REVERT: E 158 MET cc_start: 0.8448 (mmm) cc_final: 0.8223 (mmt) REVERT: E 322 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7846 (mpp80) REVERT: E 435 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7929 (pm20) REVERT: E 466 GLU cc_start: 0.7976 (tp30) cc_final: 0.7590 (tp30) REVERT: E 467 THR cc_start: 0.8940 (m) cc_final: 0.8578 (t) REVERT: E 563 PHE cc_start: 0.9331 (m-80) cc_final: 0.9086 (m-80) REVERT: E 603 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8712 (mp10) REVERT: E 745 ARG cc_start: 0.7729 (ptm160) cc_final: 0.7052 (ptm-80) REVERT: D 135 LEU cc_start: 0.8519 (tp) cc_final: 0.8274 (tp) REVERT: D 183 HIS cc_start: 0.6554 (t70) cc_final: 0.6138 (t70) REVERT: D 244 TYR cc_start: 0.8222 (p90) cc_final: 0.7914 (p90) REVERT: D 397 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 427 MET cc_start: 0.8226 (tmm) cc_final: 0.7920 (tmm) REVERT: D 543 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7961 (mtpt) REVERT: D 603 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8177 (tp-100) REVERT: C 217 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8943 (mtmm) REVERT: C 601 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6795 (mt) REVERT: C 607 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8766 (mm-30) REVERT: C 757 MET cc_start: 0.7745 (tpp) cc_final: 0.7476 (tpp) REVERT: H 338 LEU cc_start: 0.7528 (mm) cc_final: 0.6706 (tt) REVERT: H 428 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6599 (tp) REVERT: B 123 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (m) REVERT: B 312 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7483 (ttmt) REVERT: B 315 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7745 (tptt) REVERT: B 321 GLU cc_start: 0.7900 (mp0) cc_final: 0.7517 (mt-10) REVERT: B 435 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7825 (pm20) REVERT: B 563 PHE cc_start: 0.9339 (m-80) cc_final: 0.9137 (m-80) REVERT: B 578 GLU cc_start: 0.8198 (tt0) cc_final: 0.7877 (tp30) REVERT: B 603 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8706 (mp10) REVERT: B 742 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.6893 (t80) REVERT: B 745 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7170 (ptm-80) REVERT: A 147 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6630 (ttt-90) REVERT: A 183 HIS cc_start: 0.6442 (t70) cc_final: 0.6029 (t70) REVERT: A 203 TYR cc_start: 0.9208 (m-80) cc_final: 0.8994 (m-80) REVERT: A 492 LEU cc_start: 0.8793 (mm) cc_final: 0.8490 (mt) REVERT: F 55 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: F 140 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7738 (tp) REVERT: F 217 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8896 (mtmm) REVERT: F 546 GLU cc_start: 0.8324 (tp30) cc_final: 0.8062 (tp30) REVERT: G 338 LEU cc_start: 0.7456 (mm) cc_final: 0.6688 (tt) REVERT: G 356 ARG cc_start: 0.5807 (ptt180) cc_final: 0.5558 (ptt-90) outliers start: 144 outliers final: 94 residues processed: 616 average time/residue: 0.2148 time to fit residues: 218.6492 Evaluate side-chains 564 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 459 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 268 optimal weight: 0.6980 chunk 446 optimal weight: 3.9990 chunk 481 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 444 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN B 317 HIS ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.158268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121618 restraints weight = 75973.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120884 restraints weight = 48693.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121610 restraints weight = 36000.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122394 restraints weight = 31212.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122769 restraints weight = 27659.529| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40156 Z= 0.168 Angle : 0.647 9.976 54294 Z= 0.315 Chirality : 0.046 0.199 6124 Planarity : 0.005 0.092 7116 Dihedral : 8.213 138.542 5544 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.01 % Allowed : 15.44 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 4954 helix: 1.41 (0.11), residues: 2242 sheet: 0.31 (0.18), residues: 806 loop : 0.40 (0.15), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 424 TYR 0.026 0.002 TYR C 244 PHE 0.021 0.001 PHE B 674 TRP 0.019 0.002 TRP C 551 HIS 0.009 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00396 (40156) covalent geometry : angle 0.64735 (54294) hydrogen bonds : bond 0.03745 ( 1857) hydrogen bonds : angle 4.32970 ( 5220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 504 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 322 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7784 (mpp80) REVERT: E 435 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7946 (pm20) REVERT: E 577 ASP cc_start: 0.8548 (t0) cc_final: 0.8105 (p0) REVERT: E 578 GLU cc_start: 0.8503 (tp30) cc_final: 0.8226 (tp30) REVERT: E 603 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8714 (mp10) REVERT: E 745 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7038 (ptm-80) REVERT: D 135 LEU cc_start: 0.8442 (tp) cc_final: 0.8186 (tp) REVERT: D 183 HIS cc_start: 0.6568 (t70) cc_final: 0.6148 (t70) REVERT: D 244 TYR cc_start: 0.8122 (p90) cc_final: 0.7850 (p90) REVERT: D 397 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8323 (tm-30) REVERT: D 427 MET cc_start: 0.8301 (tmm) cc_final: 0.7974 (tmm) REVERT: D 492 LEU cc_start: 0.8666 (mm) cc_final: 0.8396 (mt) REVERT: D 543 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7931 (mtpt) REVERT: C 167 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6963 (tp30) REVERT: C 217 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8866 (mtmm) REVERT: C 607 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8741 (mm-30) REVERT: C 757 MET cc_start: 0.7568 (tpp) cc_final: 0.7307 (tpp) REVERT: H 338 LEU cc_start: 0.7519 (mm) cc_final: 0.6833 (tt) REVERT: B 123 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 315 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7691 (tptt) REVERT: B 563 PHE cc_start: 0.9292 (m-80) cc_final: 0.9077 (m-80) REVERT: B 578 GLU cc_start: 0.8132 (tt0) cc_final: 0.7900 (tm-30) REVERT: B 603 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8193 (mp10) REVERT: B 742 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6816 (t80) REVERT: B 745 ARG cc_start: 0.7777 (ptm160) cc_final: 0.7105 (ptm-80) REVERT: A 183 HIS cc_start: 0.6465 (t70) cc_final: 0.6044 (t70) REVERT: A 492 LEU cc_start: 0.8765 (mm) cc_final: 0.8465 (mt) REVERT: F 217 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8877 (mtmm) REVERT: F 546 GLU cc_start: 0.8319 (tp30) cc_final: 0.8074 (tp30) REVERT: G 338 LEU cc_start: 0.7535 (mm) cc_final: 0.6814 (tt) outliers start: 128 outliers final: 90 residues processed: 591 average time/residue: 0.2141 time to fit residues: 209.5778 Evaluate side-chains 557 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 461 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 412 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 336 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 486 optimal weight: 3.9990 chunk 411 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 252 optimal weight: 0.0980 chunk 406 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 641 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN C 183 HIS C 603 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN F 421 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.161535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124367 restraints weight = 75638.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123754 restraints weight = 48333.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125413 restraints weight = 36222.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125841 restraints weight = 29941.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126251 restraints weight = 25657.040| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 40156 Z= 0.116 Angle : 0.624 9.647 54294 Z= 0.303 Chirality : 0.044 0.226 6124 Planarity : 0.005 0.086 7116 Dihedral : 7.911 145.577 5544 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.14 % Allowed : 16.43 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 4954 helix: 1.54 (0.11), residues: 2234 sheet: 0.30 (0.18), residues: 834 loop : 0.52 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 147 TYR 0.027 0.002 TYR C 244 PHE 0.025 0.001 PHE G 377 TRP 0.018 0.001 TRP C 551 HIS 0.024 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00260 (40156) covalent geometry : angle 0.62351 (54294) hydrogen bonds : bond 0.03371 ( 1857) hydrogen bonds : angle 4.16362 ( 5220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 547 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 427 MET cc_start: 0.5005 (tpt) cc_final: 0.4484 (tpt) REVERT: E 435 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7855 (pm20) REVERT: E 466 GLU cc_start: 0.7634 (tp30) cc_final: 0.7281 (tp30) REVERT: E 542 ILE cc_start: 0.8704 (mm) cc_final: 0.8390 (mm) REVERT: E 543 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7877 (ptmm) REVERT: E 563 PHE cc_start: 0.9255 (m-80) cc_final: 0.9053 (m-80) REVERT: E 577 ASP cc_start: 0.8417 (t0) cc_final: 0.8078 (p0) REVERT: E 603 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8402 (mp10) REVERT: E 745 ARG cc_start: 0.7631 (ptm160) cc_final: 0.7046 (mtm180) REVERT: D 30 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7925 (mm-30) REVERT: D 135 LEU cc_start: 0.8379 (tp) cc_final: 0.8083 (tp) REVERT: D 183 HIS cc_start: 0.6458 (t70) cc_final: 0.6020 (t70) REVERT: D 244 TYR cc_start: 0.8029 (p90) cc_final: 0.7750 (p90) REVERT: D 397 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 427 MET cc_start: 0.8301 (tmm) cc_final: 0.7978 (tmm) REVERT: D 492 LEU cc_start: 0.8613 (mm) cc_final: 0.8379 (mt) REVERT: C 495 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.4816 (t80) REVERT: C 607 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8756 (mm-30) REVERT: C 757 MET cc_start: 0.7511 (tpp) cc_final: 0.7280 (tpp) REVERT: H 160 LYS cc_start: 0.3419 (mtpt) cc_final: 0.2722 (tmtt) REVERT: H 338 LEU cc_start: 0.7367 (mm) cc_final: 0.6783 (tt) REVERT: B 123 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8485 (m) REVERT: B 315 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7912 (tptt) REVERT: B 603 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8226 (mp10) REVERT: B 742 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6770 (t80) REVERT: B 745 ARG cc_start: 0.7665 (ptm160) cc_final: 0.6961 (ptm-80) REVERT: A 183 HIS cc_start: 0.6448 (t70) cc_final: 0.6024 (t70) REVERT: A 492 LEU cc_start: 0.8713 (mm) cc_final: 0.8435 (mt) REVERT: A 550 MET cc_start: 0.3444 (tpp) cc_final: 0.3018 (tmm) REVERT: F 546 GLU cc_start: 0.8276 (tp30) cc_final: 0.8008 (tp30) REVERT: F 629 ILE cc_start: 0.8811 (tt) cc_final: 0.8594 (mm) REVERT: G 338 LEU cc_start: 0.7419 (mm) cc_final: 0.6782 (tt) outliers start: 91 outliers final: 58 residues processed: 604 average time/residue: 0.2235 time to fit residues: 223.4554 Evaluate side-chains 554 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 736 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 690 ILE Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 164 optimal weight: 0.6980 chunk 409 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 451 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 349 optimal weight: 2.9990 chunk 407 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 285 ASN E 641 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.160643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123123 restraints weight = 75908.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123065 restraints weight = 47798.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124372 restraints weight = 33894.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124715 restraints weight = 30127.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124929 restraints weight = 26011.950| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 40156 Z= 0.128 Angle : 0.636 10.554 54294 Z= 0.308 Chirality : 0.045 0.252 6124 Planarity : 0.004 0.083 7116 Dihedral : 7.791 148.844 5544 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 17.00 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.34 (0.12), residues: 4954 helix: 1.55 (0.11), residues: 2238 sheet: 0.38 (0.18), residues: 828 loop : 0.50 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 147 TYR 0.030 0.002 TYR E 495 PHE 0.040 0.001 PHE B 674 TRP 0.018 0.001 TRP C 551 HIS 0.028 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00300 (40156) covalent geometry : angle 0.63649 (54294) hydrogen bonds : bond 0.03354 ( 1857) hydrogen bonds : angle 4.16985 ( 5220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 511 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 VAL cc_start: 0.9320 (t) cc_final: 0.8911 (p) REVERT: E 123 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8476 (m) REVERT: E 203 TYR cc_start: 0.9049 (m-10) cc_final: 0.8750 (m-80) REVERT: E 435 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7905 (pm20) REVERT: E 466 GLU cc_start: 0.7692 (tp30) cc_final: 0.7336 (tp30) REVERT: E 542 ILE cc_start: 0.8675 (mm) cc_final: 0.8354 (mm) REVERT: E 543 LYS cc_start: 0.8398 (ptmt) cc_final: 0.7875 (ptmm) REVERT: E 563 PHE cc_start: 0.9261 (m-80) cc_final: 0.9016 (m-80) REVERT: E 577 ASP cc_start: 0.8474 (t0) cc_final: 0.8068 (p0) REVERT: E 578 GLU cc_start: 0.8295 (tp30) cc_final: 0.8084 (tp30) REVERT: E 603 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8416 (mp10) REVERT: E 745 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7077 (mtm180) REVERT: D 30 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7919 (mm-30) REVERT: D 135 LEU cc_start: 0.8403 (tp) cc_final: 0.8096 (tp) REVERT: D 158 MET cc_start: 0.8332 (mmm) cc_final: 0.8101 (mmt) REVERT: D 183 HIS cc_start: 0.6531 (t70) cc_final: 0.6055 (t-90) REVERT: D 244 TYR cc_start: 0.8031 (p90) cc_final: 0.7735 (p90) REVERT: D 397 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 427 MET cc_start: 0.8307 (tmm) cc_final: 0.7976 (tmm) REVERT: D 492 LEU cc_start: 0.8630 (mm) cc_final: 0.8400 (mt) REVERT: C 140 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7693 (tt) REVERT: C 757 MET cc_start: 0.7462 (tpp) cc_final: 0.7241 (tpp) REVERT: B 38 VAL cc_start: 0.9267 (t) cc_final: 0.8841 (p) REVERT: B 123 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (m) REVERT: B 315 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7613 (tptt) REVERT: B 563 PHE cc_start: 0.9230 (m-80) cc_final: 0.9012 (m-80) REVERT: B 578 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 603 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8360 (mp10) REVERT: B 634 LEU cc_start: 0.8804 (mm) cc_final: 0.8583 (mm) REVERT: B 742 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 745 ARG cc_start: 0.7715 (ptm160) cc_final: 0.6988 (ptm-80) REVERT: A 183 HIS cc_start: 0.6580 (t70) cc_final: 0.6110 (t-90) REVERT: A 492 LEU cc_start: 0.8718 (mm) cc_final: 0.8446 (mt) REVERT: F 546 GLU cc_start: 0.8305 (tp30) cc_final: 0.8042 (tp30) REVERT: F 629 ILE cc_start: 0.8813 (tt) cc_final: 0.8538 (mm) REVERT: G 338 LEU cc_start: 0.7446 (mm) cc_final: 0.6828 (tt) outliers start: 83 outliers final: 58 residues processed: 568 average time/residue: 0.2246 time to fit residues: 211.1238 Evaluate side-chains 544 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 482 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 736 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 24 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 420 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 457 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 372 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 294 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 641 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN C 603 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** F 602 ASN ** 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 = 0.4109 r_free = 0.4109 target = 0.156792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118806 restraints weight = 75640.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117202 restraints weight = 49088.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.119385 restraints weight = 37682.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119371 restraints weight = 29237.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119798 restraints weight = 26254.466| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 40156 Z= 0.177 Angle : 0.672 11.803 54294 Z= 0.326 Chirality : 0.046 0.227 6124 Planarity : 0.005 0.082 7116 Dihedral : 7.779 149.627 5544 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.00 % Allowed : 17.18 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.29 (0.12), residues: 4954 helix: 1.54 (0.11), residues: 2238 sheet: 0.29 (0.18), residues: 808 loop : 0.47 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 147 TYR 0.033 0.002 TYR E 495 PHE 0.023 0.001 PHE B 674 TRP 0.019 0.001 TRP F 551 HIS 0.035 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00422 (40156) covalent geometry : angle 0.67166 (54294) hydrogen bonds : bond 0.03559 ( 1857) hydrogen bonds : angle 4.28462 ( 5220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 493 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 VAL cc_start: 0.9377 (t) cc_final: 0.8959 (p) REVERT: E 84 MET cc_start: 0.7812 (ptm) cc_final: 0.7561 (ptm) REVERT: E 123 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8467 (m) REVERT: E 203 TYR cc_start: 0.9129 (m-10) cc_final: 0.8844 (m-80) REVERT: E 304 ASP cc_start: 0.8602 (t0) cc_final: 0.8367 (t0) REVERT: E 322 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7733 (mpp80) REVERT: E 427 MET cc_start: 0.4937 (tpt) cc_final: 0.4499 (tpt) REVERT: E 435 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7964 (pm20) REVERT: E 466 GLU cc_start: 0.7793 (tp30) cc_final: 0.7522 (tp30) REVERT: E 542 ILE cc_start: 0.8670 (mm) cc_final: 0.8276 (mm) REVERT: E 543 LYS cc_start: 0.8563 (ptmt) cc_final: 0.7817 (ptmm) REVERT: E 563 PHE cc_start: 0.9369 (m-80) cc_final: 0.9089 (m-80) REVERT: E 577 ASP cc_start: 0.8547 (t0) cc_final: 0.7992 (p0) REVERT: E 578 GLU cc_start: 0.8284 (tp30) cc_final: 0.8032 (tp30) REVERT: E 603 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8380 (mp10) REVERT: E 745 ARG cc_start: 0.7687 (ptm160) cc_final: 0.6949 (ptm-80) REVERT: D 29 ASP cc_start: 0.8053 (t0) cc_final: 0.7838 (t70) REVERT: D 30 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 135 LEU cc_start: 0.8495 (tp) cc_final: 0.8203 (tp) REVERT: D 158 MET cc_start: 0.8454 (mmm) cc_final: 0.8241 (mmt) REVERT: D 183 HIS cc_start: 0.6566 (t70) cc_final: 0.6093 (t-90) REVERT: D 244 TYR cc_start: 0.8132 (p90) cc_final: 0.7850 (p90) REVERT: D 397 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8337 (tm-30) REVERT: D 427 MET cc_start: 0.8252 (tmm) cc_final: 0.7889 (tmm) REVERT: D 492 LEU cc_start: 0.8626 (mm) cc_final: 0.8365 (mt) REVERT: C 495 TYR cc_start: 0.5108 (OUTLIER) cc_final: 0.4829 (t80) REVERT: C 757 MET cc_start: 0.7561 (tpp) cc_final: 0.7303 (tpp) REVERT: H 338 LEU cc_start: 0.7320 (mm) cc_final: 0.6656 (tt) REVERT: H 387 LEU cc_start: 0.8246 (mt) cc_final: 0.7838 (mp) REVERT: B 123 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 315 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7655 (tptt) REVERT: B 321 GLU cc_start: 0.7802 (mp0) cc_final: 0.7508 (mt-10) REVERT: B 563 PHE cc_start: 0.9334 (m-80) cc_final: 0.9008 (m-80) REVERT: B 578 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 603 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8329 (mp10) REVERT: B 634 LEU cc_start: 0.8888 (mm) cc_final: 0.8666 (mm) REVERT: B 671 ASP cc_start: 0.8231 (t0) cc_final: 0.7314 (p0) REVERT: B 742 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 745 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7016 (ptm-80) REVERT: A 183 HIS cc_start: 0.6676 (t70) cc_final: 0.6158 (t-90) REVERT: A 424 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8486 (mmt90) REVERT: A 492 LEU cc_start: 0.8756 (mm) cc_final: 0.8461 (mt) REVERT: F 546 GLU cc_start: 0.8391 (tp30) cc_final: 0.8152 (tp30) REVERT: F 629 ILE cc_start: 0.8834 (tt) cc_final: 0.8554 (mm) REVERT: G 338 LEU cc_start: 0.7362 (mm) cc_final: 0.6718 (tt) outliers start: 85 outliers final: 63 residues processed: 559 average time/residue: 0.2101 time to fit residues: 195.7183 Evaluate side-chains 546 residues out of total 4248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 477 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 386 LYS Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 690 ILE Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 451 optimal weight: 0.9990 chunk 461 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 422 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 chunk 389 optimal weight: 9.9990 chunk 443 optimal weight: 8.9990 chunk 297 optimal weight: 0.2980 chunk 227 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 GLN D 36 ASN D 103 GLN ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN C 603 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.160965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124526 restraints weight = 75799.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123594 restraints weight = 48737.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125156 restraints weight = 35575.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125638 restraints weight = 27765.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125800 restraints weight = 25198.573| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 40156 Z= 0.129 Angle : 0.644 11.583 54294 Z= 0.311 Chirality : 0.045 0.223 6124 Planarity : 0.004 0.081 7116 Dihedral : 7.588 150.341 5544 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.91 % Allowed : 17.26 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 4954 helix: 1.61 (0.11), residues: 2234 sheet: 0.35 (0.18), residues: 812 loop : 0.50 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 147 TYR 0.030 0.002 TYR C 244 PHE 0.027 0.001 PHE B 674 TRP 0.020 0.001 TRP F 551 HIS 0.012 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00306 (40156) covalent geometry : angle 0.64445 (54294) hydrogen bonds : bond 0.03297 ( 1857) hydrogen bonds : angle 4.20509 ( 5220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7718.76 seconds wall clock time: 133 minutes 30.97 seconds (8010.97 seconds total)