Starting phenix.real_space_refine on Mon Oct 13 11:27:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k92_36972/10_2025/8k92_36972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k92_36972/10_2025/8k92_36972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k92_36972/10_2025/8k92_36972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k92_36972/10_2025/8k92_36972.map" model { file = "/net/cci-nas-00/data/ceres_data/8k92_36972/10_2025/8k92_36972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k92_36972/10_2025/8k92_36972.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.034 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 6 5.49 5 S 48 5.16 5 C 21150 2.51 5 N 6000 2.21 5 O 6276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33480 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.72, per 1000 atoms: 0.23 Number of scatterers: 33480 At special positions: 0 Unit cell: (137.76, 140.22, 163.18, 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 48 16.00 P 6 15.00 O 6276 8.00 N 6000 7.00 C 21150 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: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 61 sheets defined 54.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.737A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.200A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.696A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.760A pdb=" N GLN A 306 " --> pdb=" O HIS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.717A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.802A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 436 through 452 removed outlier: 3.520A pdb=" N ILE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.900A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.645A pdb=" N TYR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 597 Processing helix chain 'A' and resid 621 through 637 Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.358A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 654 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 70 removed outlier: 3.733A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 111 removed outlier: 4.350A pdb=" N HIS F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.837A pdb=" N PHE F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 154 Processing helix chain 'F' and resid 173 through 221 removed outlier: 3.985A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'F' and resid 246 through 250 removed outlier: 3.670A pdb=" N TRP F 250 " --> pdb=" O PRO F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.777A pdb=" N GLN F 306 " --> pdb=" O HIS F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 369 Processing helix chain 'F' and resid 373 through 380 removed outlier: 3.608A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 378 " --> pdb=" O PRO F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 408 Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 436 through 451 removed outlier: 3.515A pdb=" N ILE F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 471 removed outlier: 3.752A pdb=" N SER F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 539 through 557 Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 649 through 651 No H-bonds generated for 'chain 'F' and resid 649 through 651' Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 Processing helix chain 'F' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.587A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 119 removed outlier: 4.555A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 154 Processing helix chain 'E' and resid 173 through 221 removed outlier: 3.509A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.926A pdb=" N GLN E 306 " --> pdb=" O HIS E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.722A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.732A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.812A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 539 through 557 removed outlier: 3.641A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.492A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 654 " --> pdb=" O LEU E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.671A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.420A pdb=" N HIS D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 118 Processing helix chain 'D' and resid 121 through 154 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.272A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.653A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 436 through 452 removed outlier: 3.566A pdb=" N ILE D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.682A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 539 through 557 Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 651 No H-bonds generated for 'chain 'D' and resid 649 through 651' Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.573A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 119 removed outlier: 4.306A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 154 Processing helix chain 'C' and resid 173 through 221 removed outlier: 3.570A pdb=" N ALA C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.794A pdb=" N GLN C 306 " --> pdb=" O HIS C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.977A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.996A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 452 removed outlier: 3.627A pdb=" N ILE C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.892A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 539 through 557 Processing helix chain 'C' and resid 583 through 597 Processing helix chain 'C' and resid 621 through 637 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.544A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.619A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.599A pdb=" N PHE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 154 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.064A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.064A pdb=" N ARG B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.574A pdb=" N ILE B 297 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.634A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.930A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.697A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 539 through 557 Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.565A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.415A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU A 269 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 93 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 4.036A pdb=" N ALA A 156 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 167 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 165 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 163 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.804A pdb=" N ASP A 286 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.057A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 504 removed outlier: 3.889A pdb=" N HIS A 527 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 604 through 606 removed outlier: 6.324A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AB3, first strand: chain 'F' and resid 266 through 269 removed outlier: 6.487A pdb=" N VAL F 267 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASP F 313 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU F 269 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 253 through 254 removed outlier: 3.754A pdb=" N VAL F 88 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AB6, first strand: chain 'F' and resid 280 through 281 Processing sheet with id=AB7, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AB8, first strand: chain 'F' and resid 334 through 335 removed outlier: 3.943A pdb=" N VAL F 335 " --> pdb=" O PHE F 352 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE F 352 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AC1, first strand: chain 'F' and resid 410 through 411 removed outlier: 6.697A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AC3, first strand: chain 'F' and resid 527 through 530 removed outlier: 3.881A pdb=" N HIS F 527 " --> pdb=" O VAL F 565 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AC5, first strand: chain 'E' and resid 266 through 269 removed outlier: 6.368A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLU E 269 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 88 through 93 Processing sheet with id=AC7, first strand: chain 'E' and resid 156 through 160 removed outlier: 3.742A pdb=" N ALA E 156 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 167 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 158 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU E 165 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG E 163 " --> pdb=" O ASN E 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.576A pdb=" N ASP E 286 " --> pdb=" O VAL E 289 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AD1, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.174A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AD3, first strand: chain 'E' and resid 527 through 530 removed outlier: 3.952A pdb=" N HIS E 527 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU E 604 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN E 500 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 502 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 609 through 610 Processing sheet with id=AD5, first strand: chain 'D' and resid 266 through 269 removed outlier: 6.400A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLU D 269 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 256 removed outlier: 3.606A pdb=" N LEU D 255 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU D 78 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AD8, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD9, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AE1, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AE2, first strand: chain 'D' and resid 410 through 411 removed outlier: 6.847A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AE4, first strand: chain 'D' and resid 527 through 530 removed outlier: 3.954A pdb=" N HIS D 527 " --> pdb=" O VAL D 565 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AE6, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.465A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLU C 269 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AE8, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.879A pdb=" N ALA C 156 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 167 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 163 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AF1, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.703A pdb=" N ASP C 286 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AF3, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.188A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AF5, first strand: chain 'C' and resid 527 through 530 removed outlier: 4.083A pdb=" N HIS C 527 " --> pdb=" O VAL C 565 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 609 through 610 Processing sheet with id=AF7, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.329A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 88 through 93 Processing sheet with id=AF9, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AG1, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AG2, first strand: chain 'B' and resid 334 through 335 removed outlier: 3.847A pdb=" N VAL B 335 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 352 " --> pdb=" O VAL B 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AG4, first strand: chain 'B' and resid 410 through 411 removed outlier: 6.851A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AG6, first strand: chain 'B' and resid 527 through 530 removed outlier: 4.016A pdb=" N HIS B 527 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 609 through 610 1919 hydrogen bonds defined for protein. 5592 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: 7.36 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11711 1.36 - 1.51: 8835 1.51 - 1.65: 13516 1.65 - 1.80: 58 1.80 - 1.95: 20 Bond restraints: 34140 Sorted by residual: bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 ... (remaining 34135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 46159 3.46 - 6.93: 167 6.93 - 10.39: 5 10.39 - 13.85: 16 13.85 - 17.32: 9 Bond angle restraints: 46356 Sorted by residual: angle pdb=" CA PRO C 509 " pdb=" N PRO C 509 " pdb=" CD PRO C 509 " ideal model delta sigma weight residual 112.00 100.03 11.97 1.40e+00 5.10e-01 7.32e+01 angle pdb=" O1P TS6 A 801 " pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 98.15 115.47 -17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.30 -17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O1P TS6 F 801 " pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 98.15 115.24 -17.09 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.22 -17.07 3.00e+00 1.11e-01 3.24e+01 ... (remaining 46351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 18752 17.95 - 35.91: 1501 35.91 - 53.86: 275 53.86 - 71.82: 110 71.82 - 89.77: 80 Dihedral angle restraints: 20718 sinusoidal: 8388 harmonic: 12330 Sorted by residual: dihedral pdb=" CA PHE E 692 " pdb=" C PHE E 692 " pdb=" N ARG E 693 " pdb=" CA ARG E 693 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PRO C 509 " pdb=" C PRO C 509 " pdb=" N TYR C 510 " pdb=" CA TYR C 510 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LEU D 411 " pdb=" C LEU D 411 " pdb=" N THR D 412 " pdb=" CA THR D 412 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 20715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4391 0.055 - 0.111: 681 0.111 - 0.166: 76 0.166 - 0.222: 12 0.222 - 0.277: 6 Chirality restraints: 5166 Sorted by residual: chirality pdb=" CB VAL C 438 " pdb=" CA VAL C 438 " pdb=" CG1 VAL C 438 " pdb=" CG2 VAL C 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL E 438 " pdb=" CA VAL E 438 " pdb=" CG1 VAL E 438 " pdb=" CG2 VAL E 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL D 438 " pdb=" CA VAL D 438 " pdb=" CG1 VAL D 438 " pdb=" CG2 VAL D 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5163 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 508 " -0.080 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO C 509 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 509 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 509 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 363 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO F 364 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 364 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 364 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " -0.226 9.50e-02 1.11e+02 1.02e-01 6.70e+00 pdb=" NE ARG B 114 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " -0.012 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 441 2.68 - 3.23: 32333 3.23 - 3.79: 55301 3.79 - 4.34: 71441 4.34 - 4.90: 121961 Nonbonded interactions: 281477 Sorted by model distance: nonbonded pdb=" OH TYR B 552 " pdb=" OE2 GLU B 678 " model vdw 2.122 3.040 nonbonded pdb=" NH1 ARG C 202 " pdb=" O ALA C 239 " model vdw 2.146 3.120 nonbonded pdb=" OG1 THR E 518 " pdb=" OE1 GLU E 572 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR F 518 " pdb=" OE2 GLU F 572 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" OE2 GLU A 9 " model vdw 2.172 3.040 ... (remaining 281472 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.390 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.006 0.329 34140 Z= 0.319 Angle : 0.702 17.317 46356 Z= 0.371 Chirality : 0.042 0.277 5166 Planarity : 0.005 0.112 6186 Dihedral : 15.169 89.774 12798 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 0.38 % Allowed : 0.41 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.39 (0.13), residues: 4302 helix: 1.99 (0.11), residues: 2235 sheet: -0.28 (0.22), residues: 531 loop : -0.15 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 114 TYR 0.026 0.002 TYR E 271 PHE 0.029 0.001 PHE E 692 TRP 0.039 0.002 TRP B 290 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00631 (34140) covalent geometry : angle 0.70195 (46356) hydrogen bonds : bond 0.14482 ( 1919) hydrogen bonds : angle 6.12849 ( 5592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 1.362 Fit side-chains REVERT: A 57 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8629 (tt) REVERT: A 201 LEU cc_start: 0.8559 (mm) cc_final: 0.8237 (tp) REVERT: A 208 HIS cc_start: 0.7530 (m-70) cc_final: 0.7207 (m-70) REVERT: F 225 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7924 (mmm-85) REVERT: D 199 ARG cc_start: 0.7134 (mtp180) cc_final: 0.6817 (mmt90) REVERT: D 710 GLU cc_start: 0.7099 (tp30) cc_final: 0.6698 (tm-30) REVERT: C 57 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8522 (tt) REVERT: C 205 TRP cc_start: 0.5773 (t60) cc_final: 0.5544 (t-100) outliers start: 13 outliers final: 1 residues processed: 187 average time/residue: 0.2238 time to fit residues: 68.7473 Evaluate side-chains 126 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain B residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN E 212 ASN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 642 GLN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.139466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105433 restraints weight = 59766.337| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.65 r_work: 0.3285 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34140 Z= 0.163 Angle : 0.551 8.236 46356 Z= 0.280 Chirality : 0.039 0.159 5166 Planarity : 0.005 0.078 6186 Dihedral : 4.193 48.867 4806 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 0.68 % Allowed : 5.23 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.47 (0.13), residues: 4302 helix: 2.08 (0.11), residues: 2262 sheet: -0.18 (0.22), residues: 516 loop : -0.23 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 202 TYR 0.021 0.002 TYR E 50 PHE 0.033 0.001 PHE C 119 TRP 0.021 0.001 TRP B 290 HIS 0.005 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00375 (34140) covalent geometry : angle 0.55112 (46356) hydrogen bonds : bond 0.04158 ( 1919) hydrogen bonds : angle 4.74956 ( 5592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7721 (m-70) cc_final: 0.7344 (m-70) REVERT: A 426 MET cc_start: 0.9186 (mtp) cc_final: 0.8978 (mtp) REVERT: E 56 SER cc_start: 0.9004 (m) cc_final: 0.8573 (t) REVERT: E 287 ARG cc_start: 0.8030 (mpp80) cc_final: 0.7209 (ptm160) REVERT: E 572 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7236 (mt-10) REVERT: D 710 GLU cc_start: 0.7118 (tp30) cc_final: 0.6493 (tm-30) outliers start: 23 outliers final: 16 residues processed: 160 average time/residue: 0.2402 time to fit residues: 61.7129 Evaluate side-chains 141 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 11 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 424 optimal weight: 0.4980 chunk 383 optimal weight: 7.9990 chunk 420 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.139138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104826 restraints weight = 59735.171| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.29 r_work: 0.3304 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34140 Z= 0.141 Angle : 0.511 8.738 46356 Z= 0.257 Chirality : 0.038 0.199 5166 Planarity : 0.004 0.068 6186 Dihedral : 4.006 49.308 4804 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 0.76 % Allowed : 7.23 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.54 (0.13), residues: 4302 helix: 2.14 (0.10), residues: 2271 sheet: -0.22 (0.22), residues: 516 loop : -0.20 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.018 0.001 TYR E 50 PHE 0.027 0.001 PHE C 119 TRP 0.016 0.001 TRP B 205 HIS 0.004 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00323 (34140) covalent geometry : angle 0.51127 (46356) hydrogen bonds : bond 0.03712 ( 1919) hydrogen bonds : angle 4.43359 ( 5592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 TRP cc_start: 0.7591 (t-100) cc_final: 0.7366 (t-100) REVERT: A 208 HIS cc_start: 0.7743 (m-70) cc_final: 0.7425 (m-70) REVERT: E 56 SER cc_start: 0.9016 (m) cc_final: 0.8708 (t) REVERT: E 287 ARG cc_start: 0.8034 (mpp80) cc_final: 0.7245 (ptm160) REVERT: E 572 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7203 (mt-10) REVERT: D 678 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7428 (mm-30) REVERT: D 710 GLU cc_start: 0.7169 (tp30) cc_final: 0.6611 (tm-30) outliers start: 26 outliers final: 15 residues processed: 173 average time/residue: 0.2321 time to fit residues: 64.6726 Evaluate side-chains 145 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 58 optimal weight: 4.9990 chunk 247 optimal weight: 30.0000 chunk 307 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 301 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 228 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 303 HIS F 653 ASN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** 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 = 0.3911 r_free = 0.3911 target = 0.136344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102205 restraints weight = 59642.424| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.61 r_work: 0.3255 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34140 Z= 0.211 Angle : 0.563 9.141 46356 Z= 0.282 Chirality : 0.040 0.262 5166 Planarity : 0.005 0.067 6186 Dihedral : 4.118 51.142 4804 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 1.41 % Allowed : 8.20 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.40 (0.13), residues: 4302 helix: 2.03 (0.11), residues: 2277 sheet: -0.32 (0.21), residues: 522 loop : -0.28 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 490 TYR 0.020 0.002 TYR E 50 PHE 0.016 0.002 PHE C 124 TRP 0.019 0.001 TRP B 290 HIS 0.007 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00499 (34140) covalent geometry : angle 0.56295 (46356) hydrogen bonds : bond 0.03726 ( 1919) hydrogen bonds : angle 4.41092 ( 5592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7757 (m-70) cc_final: 0.7338 (m-70) REVERT: E 56 SER cc_start: 0.9105 (m) cc_final: 0.8815 (t) REVERT: E 287 ARG cc_start: 0.8106 (mpp80) cc_final: 0.7247 (ptm160) REVERT: E 572 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7272 (mt-10) REVERT: D 79 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8222 (pp) REVERT: D 201 LEU cc_start: 0.8641 (tp) cc_final: 0.8431 (tp) REVERT: D 710 GLU cc_start: 0.7156 (tp30) cc_final: 0.6563 (tm-30) REVERT: C 124 PHE cc_start: 0.5734 (t80) cc_final: 0.5357 (t80) outliers start: 48 outliers final: 26 residues processed: 177 average time/residue: 0.2315 time to fit residues: 66.6738 Evaluate side-chains 149 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 289 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 386 optimal weight: 0.6980 chunk 278 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 312 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 573 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.130925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097482 restraints weight = 59703.206| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.63 r_work: 0.3290 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34140 Z= 0.118 Angle : 0.494 10.910 46356 Z= 0.245 Chirality : 0.037 0.262 5166 Planarity : 0.004 0.068 6186 Dihedral : 3.968 49.838 4804 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 1.23 % Allowed : 9.38 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.57 (0.13), residues: 4302 helix: 2.19 (0.11), residues: 2280 sheet: -0.25 (0.21), residues: 522 loop : -0.22 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 287 TYR 0.017 0.001 TYR D 209 PHE 0.013 0.001 PHE E 629 TRP 0.011 0.001 TRP B 205 HIS 0.003 0.000 HIS D 469 Details of bonding type rmsd covalent geometry : bond 0.00267 (34140) covalent geometry : angle 0.49365 (46356) hydrogen bonds : bond 0.03430 ( 1919) hydrogen bonds : angle 4.20066 ( 5592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7696 (m-70) cc_final: 0.7284 (m-70) REVERT: F 218 PHE cc_start: 0.7250 (m-10) cc_final: 0.6739 (m-80) REVERT: F 225 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7953 (tpt90) REVERT: E 56 SER cc_start: 0.9075 (m) cc_final: 0.8752 (t) REVERT: E 287 ARG cc_start: 0.8041 (mpp80) cc_final: 0.7220 (ptm160) REVERT: E 572 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7211 (mt-10) REVERT: D 79 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 678 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7481 (mp0) REVERT: D 710 GLU cc_start: 0.7116 (tp30) cc_final: 0.6609 (tm-30) REVERT: B 708 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7709 (mmt-90) outliers start: 42 outliers final: 22 residues processed: 182 average time/residue: 0.2331 time to fit residues: 68.9883 Evaluate side-chains 147 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 363 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 241 optimal weight: 0.4980 chunk 182 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 345 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 573 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.131026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097388 restraints weight = 59496.812| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.51 r_work: 0.3300 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34140 Z= 0.120 Angle : 0.494 11.159 46356 Z= 0.244 Chirality : 0.037 0.299 5166 Planarity : 0.004 0.067 6186 Dihedral : 3.896 50.010 4804 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 1.53 % Allowed : 9.85 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.65 (0.13), residues: 4302 helix: 2.24 (0.11), residues: 2280 sheet: -0.28 (0.21), residues: 516 loop : -0.15 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 225 TYR 0.015 0.001 TYR D 209 PHE 0.017 0.001 PHE D 352 TRP 0.014 0.001 TRP B 205 HIS 0.004 0.000 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00272 (34140) covalent geometry : angle 0.49382 (46356) hydrogen bonds : bond 0.03376 ( 1919) hydrogen bonds : angle 4.13607 ( 5592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7689 (m-70) cc_final: 0.7282 (m-70) REVERT: F 79 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 56 SER cc_start: 0.9082 (m) cc_final: 0.8768 (t) REVERT: E 287 ARG cc_start: 0.8070 (mpp80) cc_final: 0.7191 (ptm160) REVERT: E 572 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7252 (mt-10) REVERT: E 659 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: D 79 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 710 GLU cc_start: 0.7088 (tp30) cc_final: 0.6609 (tm-30) REVERT: B 708 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7700 (mmt-90) outliers start: 52 outliers final: 29 residues processed: 181 average time/residue: 0.2242 time to fit residues: 66.9123 Evaluate side-chains 154 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 363 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 368 optimal weight: 30.0000 chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 302 optimal weight: 30.0000 chunk 6 optimal weight: 0.9990 chunk 356 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 483 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** B 573 GLN ** 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 = 0.3871 r_free = 0.3871 target = 0.134294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099868 restraints weight = 60731.803| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.62 r_work: 0.3196 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 34140 Z= 0.343 Angle : 0.672 10.397 46356 Z= 0.336 Chirality : 0.044 0.243 5166 Planarity : 0.005 0.064 6186 Dihedral : 4.361 53.136 4804 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 1.76 % Allowed : 10.20 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.15 (0.13), residues: 4302 helix: 1.83 (0.10), residues: 2268 sheet: -0.53 (0.21), residues: 501 loop : -0.33 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 328 TYR 0.024 0.003 TYR E 50 PHE 0.022 0.002 PHE C 352 TRP 0.027 0.002 TRP B 290 HIS 0.010 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00815 (34140) covalent geometry : angle 0.67152 (46356) hydrogen bonds : bond 0.04022 ( 1919) hydrogen bonds : angle 4.51902 ( 5592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7773 (m-70) cc_final: 0.7167 (m-70) REVERT: F 79 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (pp) REVERT: F 218 PHE cc_start: 0.7291 (m-10) cc_final: 0.6765 (m-80) REVERT: F 581 ASP cc_start: 0.8331 (p0) cc_final: 0.7835 (t0) REVERT: E 56 SER cc_start: 0.9190 (m) cc_final: 0.8884 (t) REVERT: E 287 ARG cc_start: 0.8245 (mpp80) cc_final: 0.7388 (ptm160) REVERT: E 342 GLN cc_start: 0.6065 (tp-100) cc_final: 0.5765 (pp30) REVERT: E 572 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7391 (mt-10) REVERT: E 659 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: D 201 LEU cc_start: 0.8646 (tp) cc_final: 0.8431 (tp) REVERT: D 710 GLU cc_start: 0.7277 (tp30) cc_final: 0.6756 (tm-30) REVERT: C 113 ASN cc_start: 0.7865 (m-40) cc_final: 0.7401 (p0) outliers start: 60 outliers final: 39 residues processed: 182 average time/residue: 0.2239 time to fit residues: 66.7072 Evaluate side-chains 160 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 112 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 311 optimal weight: 0.9980 chunk 325 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 483 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103763 restraints weight = 59448.206| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.64 r_work: 0.3259 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34140 Z= 0.140 Angle : 0.526 11.922 46356 Z= 0.262 Chirality : 0.038 0.287 5166 Planarity : 0.004 0.068 6186 Dihedral : 4.104 51.721 4804 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 10.88 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.13), residues: 4302 helix: 2.10 (0.11), residues: 2265 sheet: -0.39 (0.21), residues: 501 loop : -0.28 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 225 TYR 0.017 0.002 TYR E 50 PHE 0.017 0.001 PHE F 571 TRP 0.013 0.001 TRP B 290 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00321 (34140) covalent geometry : angle 0.52638 (46356) hydrogen bonds : bond 0.03522 ( 1919) hydrogen bonds : angle 4.24475 ( 5592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7766 (m-70) cc_final: 0.7360 (m-70) REVERT: F 119 PHE cc_start: 0.7587 (m-80) cc_final: 0.7240 (m-80) REVERT: F 218 PHE cc_start: 0.7096 (m-10) cc_final: 0.6589 (m-80) REVERT: F 581 ASP cc_start: 0.8331 (p0) cc_final: 0.7683 (t0) REVERT: F 611 ASP cc_start: 0.7835 (p0) cc_final: 0.7627 (p0) REVERT: E 56 SER cc_start: 0.9133 (m) cc_final: 0.8812 (t) REVERT: E 287 ARG cc_start: 0.8126 (mpp80) cc_final: 0.7258 (ptm160) REVERT: E 572 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7371 (mt-10) REVERT: E 659 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: E 693 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6633 (mmp-170) REVERT: E 711 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6239 (mt-10) REVERT: D 201 LEU cc_start: 0.8674 (tp) cc_final: 0.8351 (tp) REVERT: D 578 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8149 (tt) REVERT: D 710 GLU cc_start: 0.7202 (tp30) cc_final: 0.6622 (tm-30) REVERT: B 708 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.7674 (mmt-90) outliers start: 41 outliers final: 31 residues processed: 166 average time/residue: 0.2281 time to fit residues: 61.7415 Evaluate side-chains 160 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 407 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 GLN F 342 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** 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 = 0.3911 r_free = 0.3911 target = 0.137031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102947 restraints weight = 59567.940| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.64 r_work: 0.3252 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34140 Z= 0.170 Angle : 0.540 13.269 46356 Z= 0.266 Chirality : 0.039 0.252 5166 Planarity : 0.004 0.066 6186 Dihedral : 4.075 51.618 4804 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 1.26 % Allowed : 11.05 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.44 (0.13), residues: 4302 helix: 2.13 (0.11), residues: 2262 sheet: -0.43 (0.21), residues: 507 loop : -0.29 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 287 TYR 0.017 0.002 TYR C 50 PHE 0.014 0.001 PHE C 124 TRP 0.015 0.001 TRP B 290 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00398 (34140) covalent geometry : angle 0.53994 (46356) hydrogen bonds : bond 0.03534 ( 1919) hydrogen bonds : angle 4.22016 ( 5592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7711 (m-70) cc_final: 0.7282 (m-70) REVERT: F 119 PHE cc_start: 0.7599 (m-80) cc_final: 0.7255 (m-80) REVERT: F 218 PHE cc_start: 0.7100 (m-10) cc_final: 0.6639 (m-80) REVERT: F 581 ASP cc_start: 0.8326 (p0) cc_final: 0.7694 (t0) REVERT: E 56 SER cc_start: 0.9159 (m) cc_final: 0.8852 (t) REVERT: E 287 ARG cc_start: 0.8117 (mpp80) cc_final: 0.7232 (ptm160) REVERT: E 572 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7344 (mt-10) REVERT: E 659 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: E 693 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6673 (mmp-170) REVERT: E 711 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6223 (mt-10) REVERT: D 201 LEU cc_start: 0.8673 (tp) cc_final: 0.8352 (tp) REVERT: D 578 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8178 (tt) REVERT: D 710 GLU cc_start: 0.7185 (tp30) cc_final: 0.6600 (tm-30) REVERT: B 708 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7666 (mmt-90) outliers start: 43 outliers final: 34 residues processed: 165 average time/residue: 0.2250 time to fit residues: 60.5976 Evaluate side-chains 162 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 205 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 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 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093995 restraints weight = 61197.266| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.77 r_work: 0.3206 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34140 Z= 0.241 Angle : 0.593 12.470 46356 Z= 0.295 Chirality : 0.040 0.276 5166 Planarity : 0.005 0.065 6186 Dihedral : 4.245 52.380 4804 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 1.29 % Allowed : 11.17 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.13), residues: 4302 helix: 1.97 (0.11), residues: 2265 sheet: -0.54 (0.21), residues: 501 loop : -0.34 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 287 TYR 0.020 0.002 TYR E 50 PHE 0.016 0.002 PHE C 352 TRP 0.021 0.001 TRP B 290 HIS 0.007 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00568 (34140) covalent geometry : angle 0.59337 (46356) hydrogen bonds : bond 0.03749 ( 1919) hydrogen bonds : angle 4.35066 ( 5592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7794 (m-70) cc_final: 0.7375 (m-70) REVERT: F 119 PHE cc_start: 0.7600 (m-80) cc_final: 0.7180 (m-80) REVERT: F 218 PHE cc_start: 0.7041 (m-10) cc_final: 0.6633 (m-80) REVERT: F 581 ASP cc_start: 0.8179 (p0) cc_final: 0.7650 (t0) REVERT: F 689 MET cc_start: 0.8332 (mtm) cc_final: 0.8126 (mtt) REVERT: E 56 SER cc_start: 0.9012 (m) cc_final: 0.8688 (t) REVERT: E 287 ARG cc_start: 0.8089 (mpp80) cc_final: 0.7323 (ptm160) REVERT: E 659 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: E 693 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6658 (mmp-170) REVERT: D 201 LEU cc_start: 0.8688 (tp) cc_final: 0.8450 (tp) REVERT: D 578 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8180 (tt) REVERT: D 710 GLU cc_start: 0.7193 (tp30) cc_final: 0.6676 (tm-30) REVERT: C 113 ASN cc_start: 0.7800 (m-40) cc_final: 0.7410 (p0) outliers start: 44 outliers final: 33 residues processed: 169 average time/residue: 0.2225 time to fit residues: 62.0176 Evaluate side-chains 159 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 363 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 322 optimal weight: 0.9990 chunk 337 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 370 optimal weight: 40.0000 chunk 375 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 211 ASN F 253 ASN E 342 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS C 223 GLN ** B 573 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103749 restraints weight = 59592.545| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.63 r_work: 0.3272 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34140 Z= 0.124 Angle : 0.519 12.801 46356 Z= 0.256 Chirality : 0.038 0.290 5166 Planarity : 0.004 0.068 6186 Dihedral : 4.060 50.675 4804 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 1.21 % Allowed : 11.35 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.52 (0.13), residues: 4302 helix: 2.20 (0.11), residues: 2265 sheet: -0.42 (0.21), residues: 507 loop : -0.26 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 287 TYR 0.017 0.001 TYR D 209 PHE 0.016 0.001 PHE E 571 TRP 0.013 0.001 TRP B 205 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00283 (34140) covalent geometry : angle 0.51935 (46356) hydrogen bonds : bond 0.03434 ( 1919) hydrogen bonds : angle 4.16089 ( 5592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8285.77 seconds wall clock time: 142 minutes 23.55 seconds (8543.55 seconds total)