Starting phenix.real_space_refine on Sun Jun 22 11:31:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d5c_27208/06_2025/8d5c_27208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d5c_27208/06_2025/8d5c_27208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d5c_27208/06_2025/8d5c_27208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d5c_27208/06_2025/8d5c_27208.map" model { file = "/net/cci-nas-00/data/ceres_data/8d5c_27208/06_2025/8d5c_27208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d5c_27208/06_2025/8d5c_27208.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.027 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 S 135 5.16 5 C 13464 2.51 5 N 3669 2.21 5 O 4102 1.98 5 H 4739 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26109 Number of models: 1 Model: "" Number of chains: 15 Chain: "X" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "Y" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "Z" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "B" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "C" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2952 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 356} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1790 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Chain: "I" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1766 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Chain: "P" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1523 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 3 Chain: "Q" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1646 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 13.55, per 1000 atoms: 0.52 Number of scatterers: 26109 At special positions: 0 Unit cell: (145.41, 180.93, 198.69, 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 135 16.00 O 4102 8.00 N 3669 7.00 C 13464 6.00 H 4739 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 130 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 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: 5.93 Conformation dependent library (CDL) restraints added in 2.6 seconds 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 44 sheets defined 19.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'X' and resid 529 through 547 removed outlier: 4.109A pdb=" N THR X 538 " --> pdb=" O SER X 534 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL X 539 " --> pdb=" O MET X 535 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY X 547 " --> pdb=" O LEU X 543 " (cutoff:3.500A) Processing helix chain 'X' and resid 568 through 593 removed outlier: 3.782A pdb=" N GLY X 572 " --> pdb=" O LEU X 568 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE X 573 " --> pdb=" O THR X 569 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA X 578 " --> pdb=" O LYS X 574 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 625 removed outlier: 3.565A pdb=" N ILE X 622 " --> pdb=" O THR X 618 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 635 Processing helix chain 'X' and resid 640 through 664 removed outlier: 3.918A pdb=" N THR X 644 " --> pdb=" O GLN X 640 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU X 663 " --> pdb=" O GLU X 659 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 546 removed outlier: 3.603A pdb=" N THR Y 538 " --> pdb=" O SER Y 534 " (cutoff:3.500A) Processing helix chain 'Y' and resid 565 through 567 No H-bonds generated for 'chain 'Y' and resid 565 through 567' Processing helix chain 'Y' and resid 568 through 593 removed outlier: 3.582A pdb=" N GLY Y 572 " --> pdb=" O LEU Y 568 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 625 removed outlier: 3.731A pdb=" N TRP Y 623 " --> pdb=" O ILE Y 619 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN Y 625 " --> pdb=" O GLU Y 621 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 635 Processing helix chain 'Y' and resid 638 through 664 removed outlier: 3.658A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 546 removed outlier: 3.695A pdb=" N VAL Z 539 " --> pdb=" O MET Z 535 " (cutoff:3.500A) Processing helix chain 'Z' and resid 567 through 593 removed outlier: 4.671A pdb=" N TRP Z 571 " --> pdb=" O GLN Z 567 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA Z 578 " --> pdb=" O LYS Z 574 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 625 Processing helix chain 'Z' and resid 627 through 635 Processing helix chain 'Z' and resid 638 through 664 removed outlier: 3.841A pdb=" N ILE Z 642 " --> pdb=" O TYR Z 638 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR Z 643 " --> pdb=" O THR Z 639 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Z 662 " --> pdb=" O GLN Z 658 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU Z 663 " --> pdb=" O GLU Z 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 100 through 113 removed outlier: 4.101A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 removed outlier: 4.185A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.798A pdb=" N THR A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.002A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.977A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 65 " --> pdb=" O TRP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.141A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 351 removed outlier: 4.508A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 Processing helix chain 'E' and resid 75 through 79 removed outlier: 3.656A pdb=" N SER E 79 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'C' and resid 64 through 73 Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.667A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.616A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.007A pdb=" N THR C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.526A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.787A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 65 removed outlier: 4.593A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 150 through 154 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.041A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.738A pdb=" N ASP J 82 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 83 " --> pdb=" O GLU J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'P' and resid 61 through 64 removed outlier: 4.255A pdb=" N MET P 64 " --> pdb=" O GLU P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'Z' and resid 604 through 609 removed outlier: 3.766A pdb=" N CYS Z 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR Z 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL C 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 removed outlier: 4.261A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.519A pdb=" N LYS A 490 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.539A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.795A pdb=" N VAL A 120 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 434 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 126 Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.592A pdb=" N THR A 257 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.592A pdb=" N THR A 257 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.310A pdb=" N VAL D 4 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.850A pdb=" N GLN D 40 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'B' and resid 35 through 39 removed outlier: 3.611A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.527A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 218 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.775A pdb=" N ILE B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 196 through 202 removed outlier: 3.994A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 434 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 122 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 432 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 9.978A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 469 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.539A pdb=" N ILE B 333 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 414 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 384 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 2 through 5 removed outlier: 4.126A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS E 29 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 28 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 37 " --> pdb=" O TRP E 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.709A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.523A pdb=" N GLN E 112 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN E 148 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 139 through 140 Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.574A pdb=" N ILE C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.848A pdb=" N THR C 455 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 469 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.127A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.961A pdb=" N LYS F 2 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 29 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AD3, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AD4, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.226A pdb=" N GLN F 112 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN F 148 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 139 through 140 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.515A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 46 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 14 removed outlier: 7.065A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.578A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET I 20 " --> pdb=" O MET I 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR I 79 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.102A pdb=" N ILE I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.147A pdb=" N VAL J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.523A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.522A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG P 40 " --> pdb=" O GLY P 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 14 removed outlier: 3.619A pdb=" N ALA Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O MET Q 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR Q 49 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN Q 53 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.88 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4739 1.04 - 1.23: 1539 1.23 - 1.43: 7737 1.43 - 1.63: 12356 1.63 - 1.83: 183 Bond restraints: 26554 Sorted by residual: bond pdb=" C TYR P 52 " pdb=" O TYR P 52 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.69e+00 bond pdb=" CA GLY I 44 " pdb=" C GLY I 44 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.19e+00 bond pdb=" CB PRO I 14 " pdb=" CG PRO I 14 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.11e+00 bond pdb=" N GLY I 44 " pdb=" CA GLY I 44 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.94e-01 bond pdb=" C GLN A 428 " pdb=" N GLY A 429 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.55e-01 ... (remaining 26549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 39716 1.54 - 3.08: 537 3.08 - 4.61: 47 4.61 - 6.15: 5 6.15 - 7.69: 2 Bond angle restraints: 40307 Sorted by residual: angle pdb=" C ALA A 73 " pdb=" N CYS A 74 " pdb=" CA CYS A 74 " ideal model delta sigma weight residual 122.19 129.88 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" C ALA C 73 " pdb=" N CYS C 74 " pdb=" CA CYS C 74 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N GLU D 150 " pdb=" CA GLU D 150 " pdb=" C GLU D 150 " ideal model delta sigma weight residual 108.34 111.59 -3.25 1.31e+00 5.83e-01 6.17e+00 angle pdb=" N PHE H 51 " pdb=" CA PHE H 51 " pdb=" CB PHE H 51 " ideal model delta sigma weight residual 111.20 115.18 -3.98 1.62e+00 3.81e-01 6.03e+00 angle pdb=" N GLY I 106 " pdb=" CA GLY I 106 " pdb=" C GLY I 106 " ideal model delta sigma weight residual 111.85 114.38 -2.53 1.06e+00 8.90e-01 5.70e+00 ... (remaining 40302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13663 17.96 - 35.93: 983 35.93 - 53.89: 210 53.89 - 71.86: 63 71.86 - 89.82: 25 Dihedral angle restraints: 14944 sinusoidal: 6650 harmonic: 8294 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -170.62 84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -169.42 83.42 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.19 -77.19 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 14941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2247 0.032 - 0.065: 728 0.065 - 0.097: 167 0.097 - 0.130: 159 0.130 - 0.162: 9 Chirality restraints: 3310 Sorted by residual: chirality pdb=" CA ILE I 48 " pdb=" N ILE I 48 " pdb=" C ILE I 48 " pdb=" CB ILE I 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CG LEU I 45 " pdb=" CB LEU I 45 " pdb=" CD1 LEU I 45 " pdb=" CD2 LEU I 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL I 37 " pdb=" N VAL I 37 " pdb=" C VAL I 37 " pdb=" CB VAL I 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3307 not shown) Planarity restraints: 4424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 51 " -0.024 2.00e-02 2.50e+03 1.67e-02 8.34e+00 pdb=" CG PHE H 51 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE H 51 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE H 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 51 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 51 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE H 51 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE H 51 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE H 51 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE H 51 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE H 51 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE H 51 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " -0.018 2.00e-02 2.50e+03 1.12e-02 5.02e+00 pdb=" CG TRP H 33 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 33 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP H 33 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 33 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 33 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP H 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 497 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 498 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " -0.024 5.00e-02 4.00e+02 ... (remaining 4421 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 466 2.17 - 2.78: 22158 2.78 - 3.39: 44282 3.39 - 3.99: 62846 3.99 - 4.60: 89864 Nonbonded interactions: 219616 Sorted by model distance: nonbonded pdb=" OG1 THR I 70 " pdb="HE22 GLN I 81 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP Q 27C" pdb=" HG SER Q 31 " model vdw 1.612 2.450 nonbonded pdb=" OE1 GLN I 39 " pdb=" HH TYR I 91 " model vdw 1.639 2.450 nonbonded pdb=" HG1 THR L 20 " pdb=" OD1 ASN L 74 " model vdw 1.643 2.450 nonbonded pdb=" HZ1 LYS J 39 " pdb=" OE1 GLN J 42 " model vdw 1.667 2.450 ... (remaining 219611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 1 through 71 or resid 76 through 114)) selection = (chain 'I' and (resid 1 through 25 or resid 27 through 93 or (resid 94 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 95 \ through 114)) } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.600 Extract box with map and model: 1.020 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.020 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.002 0.053 21855 Z= 0.101 Angle : 0.478 7.689 29683 Z= 0.268 Chirality : 0.040 0.162 3310 Planarity : 0.003 0.043 3790 Dihedral : 13.149 89.821 7924 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 32.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2666 helix: 1.65 (0.28), residues: 405 sheet: -0.85 (0.19), residues: 708 loop : -2.02 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 33 HIS 0.005 0.001 HIS A 374 PHE 0.049 0.001 PHE H 51 TYR 0.015 0.001 TYR H 97 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.17680 ( 699) hydrogen bonds : angle 6.47612 ( 1815) SS BOND : bond 0.00338 ( 40) SS BOND : angle 0.99311 ( 80) covalent geometry : bond 0.00202 (21815) covalent geometry : angle 0.47587 (29603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7944 (mmm) cc_final: 0.7698 (mmp) REVERT: E 78 ASP cc_start: 0.6339 (t70) cc_final: 0.6095 (t70) REVERT: E 87 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6135 (tm-30) REVERT: F 14 LEU cc_start: 0.5947 (mm) cc_final: 0.5557 (mm) REVERT: F 70 ILE cc_start: 0.6836 (mm) cc_final: 0.6529 (mm) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3995 time to fit residues: 194.2718 Evaluate side-chains 237 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 616 ASN Z 658 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS F 89 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.169990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.147862 restraints weight = 85872.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.150957 restraints weight = 135461.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.150815 restraints weight = 52836.532| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21855 Z= 0.121 Angle : 0.485 6.488 29683 Z= 0.257 Chirality : 0.041 0.142 3310 Planarity : 0.003 0.038 3790 Dihedral : 3.950 32.275 2887 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 31.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.59 % Allowed : 6.46 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2666 helix: 1.41 (0.27), residues: 423 sheet: -0.80 (0.20), residues: 702 loop : -2.12 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 96 HIS 0.010 0.001 HIS P 43 PHE 0.019 0.001 PHE H 51 TYR 0.017 0.001 TYR H 97 ARG 0.003 0.000 ARG I 13 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 699) hydrogen bonds : angle 5.66338 ( 1815) SS BOND : bond 0.00399 ( 40) SS BOND : angle 1.16371 ( 80) covalent geometry : bond 0.00272 (21815) covalent geometry : angle 0.48179 (29603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 251 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8474 (p) cc_final: 0.8149 (t) REVERT: Z 589 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7319 (t0) REVERT: A 475 MET cc_start: 0.7588 (mmm) cc_final: 0.7291 (mmp) REVERT: E 87 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6073 (tm-30) outliers start: 14 outliers final: 11 residues processed: 261 average time/residue: 0.4203 time to fit residues: 173.0695 Evaluate side-chains 245 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 539 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 155 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 567 GLN ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.165444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.143974 restraints weight = 85899.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.146840 restraints weight = 143642.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.146915 restraints weight = 56308.110| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21855 Z= 0.199 Angle : 0.584 8.849 29683 Z= 0.307 Chirality : 0.043 0.170 3310 Planarity : 0.004 0.037 3790 Dihedral : 4.523 33.037 2887 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 36.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 1.65 % Allowed : 10.08 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2666 helix: 1.00 (0.26), residues: 423 sheet: -0.91 (0.20), residues: 696 loop : -2.27 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 112 HIS 0.008 0.001 HIS B 66 PHE 0.018 0.002 PHE B 53 TYR 0.021 0.002 TYR H 97 ARG 0.005 0.001 ARG C 503 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 699) hydrogen bonds : angle 5.79604 ( 1815) SS BOND : bond 0.00417 ( 40) SS BOND : angle 1.56733 ( 80) covalent geometry : bond 0.00464 (21815) covalent geometry : angle 0.57934 (29603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 584 GLU cc_start: 0.8105 (tp30) cc_final: 0.7898 (tp30) REVERT: Y 644 THR cc_start: 0.8469 (p) cc_final: 0.8187 (t) REVERT: Z 589 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7514 (t0) REVERT: E 87 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6166 (tm-30) REVERT: H 12 VAL cc_start: 0.6318 (t) cc_final: 0.6116 (t) outliers start: 39 outliers final: 27 residues processed: 266 average time/residue: 0.3980 time to fit residues: 166.9254 Evaluate side-chains 260 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP Chi-restraints excluded: chain Z residue 619 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 35 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 258 optimal weight: 20.0000 chunk 224 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 HIS ** J 92 HIS ** 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 = 0.4496 r_free = 0.4496 target = 0.168807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.146652 restraints weight = 85917.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.149556 restraints weight = 138838.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.149757 restraints weight = 53879.896| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 21855 Z= 0.092 Angle : 0.465 12.321 29683 Z= 0.243 Chirality : 0.040 0.220 3310 Planarity : 0.003 0.033 3790 Dihedral : 4.045 30.773 2887 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 31.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.27 % Allowed : 11.05 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2666 helix: 1.71 (0.27), residues: 405 sheet: -0.83 (0.20), residues: 702 loop : -2.13 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 96 HIS 0.005 0.001 HIS P 43 PHE 0.011 0.001 PHE H 51 TYR 0.018 0.001 TYR H 97 ARG 0.003 0.000 ARG P 94 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 699) hydrogen bonds : angle 5.34945 ( 1815) SS BOND : bond 0.00269 ( 40) SS BOND : angle 1.65548 ( 80) covalent geometry : bond 0.00210 (21815) covalent geometry : angle 0.45795 (29603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8472 (p) cc_final: 0.8171 (t) REVERT: A 475 MET cc_start: 0.7585 (mmm) cc_final: 0.7264 (mmp) REVERT: E 87 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6100 (tm-30) REVERT: C 475 MET cc_start: 0.7960 (tpp) cc_final: 0.7227 (tpp) REVERT: H 12 VAL cc_start: 0.6209 (t) cc_final: 0.6007 (t) outliers start: 30 outliers final: 20 residues processed: 266 average time/residue: 0.4534 time to fit residues: 189.9779 Evaluate side-chains 252 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 570 VAL Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 548 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN D 27 HIS ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.164782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.145324 restraints weight = 85978.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.146994 restraints weight = 142027.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.147133 restraints weight = 59674.705| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 21855 Z= 0.193 Angle : 0.576 12.392 29683 Z= 0.301 Chirality : 0.043 0.272 3310 Planarity : 0.004 0.037 3790 Dihedral : 4.473 31.724 2887 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 36.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 2.07 % Allowed : 13.04 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2666 helix: 1.31 (0.27), residues: 408 sheet: -0.90 (0.20), residues: 702 loop : -2.26 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 96 HIS 0.007 0.001 HIS B 66 PHE 0.023 0.002 PHE P 63 TYR 0.021 0.002 TYR H 97 ARG 0.005 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 699) hydrogen bonds : angle 5.60810 ( 1815) SS BOND : bond 0.00462 ( 40) SS BOND : angle 1.97443 ( 80) covalent geometry : bond 0.00454 (21815) covalent geometry : angle 0.56802 (29603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8500 (p) cc_final: 0.8223 (t) REVERT: E 87 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6253 (tm-30) REVERT: C 475 MET cc_start: 0.8155 (tpp) cc_final: 0.7298 (tpp) REVERT: H 12 VAL cc_start: 0.6201 (t) cc_final: 0.5994 (t) REVERT: Q 27 GLN cc_start: 0.2569 (tm-30) cc_final: 0.1984 (tp40) outliers start: 49 outliers final: 38 residues processed: 271 average time/residue: 0.4618 time to fit residues: 197.3431 Evaluate side-chains 274 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 570 VAL Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Y residue 573 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 619 ILE Chi-restraints excluded: chain Z residue 637 ASN Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 63 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 186 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 50 optimal weight: 0.0870 chunk 133 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS ** Q 27 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 = 0.4462 r_free = 0.4462 target = 0.165969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144609 restraints weight = 85803.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.147451 restraints weight = 145619.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.147575 restraints weight = 57060.769| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21855 Z= 0.142 Angle : 0.514 7.185 29683 Z= 0.270 Chirality : 0.042 0.171 3310 Planarity : 0.003 0.034 3790 Dihedral : 4.377 31.286 2887 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 35.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.94 % Allowed : 14.22 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.16), residues: 2666 helix: 1.42 (0.27), residues: 408 sheet: -0.90 (0.20), residues: 700 loop : -2.25 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.007 0.001 HIS A 66 PHE 0.020 0.002 PHE P 63 TYR 0.020 0.001 TYR H 97 ARG 0.004 0.000 ARG C 298 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 699) hydrogen bonds : angle 5.44168 ( 1815) SS BOND : bond 0.00425 ( 40) SS BOND : angle 1.47758 ( 80) covalent geometry : bond 0.00331 (21815) covalent geometry : angle 0.50846 (29603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8463 (p) cc_final: 0.8188 (t) REVERT: A 479 TRP cc_start: 0.7321 (m-10) cc_final: 0.6753 (m-10) REVERT: E 87 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6240 (tm-30) REVERT: C 475 MET cc_start: 0.8248 (tpp) cc_final: 0.7484 (tpp) REVERT: Q 27 GLN cc_start: 0.2313 (tm-30) cc_final: 0.1645 (tp40) outliers start: 46 outliers final: 39 residues processed: 277 average time/residue: 0.4638 time to fit residues: 204.5829 Evaluate side-chains 273 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 570 VAL Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 63 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 101 optimal weight: 0.2980 chunk 259 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.0050 chunk 194 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 83 optimal weight: 50.0000 chunk 230 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** Q 27 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 = 0.4483 r_free = 0.4483 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.145604 restraints weight = 85180.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.148832 restraints weight = 136462.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.148948 restraints weight = 53433.414| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 21855 Z= 0.090 Angle : 0.469 10.966 29683 Z= 0.244 Chirality : 0.041 0.310 3310 Planarity : 0.003 0.033 3790 Dihedral : 4.003 29.566 2887 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.22 % Allowed : 15.23 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2666 helix: 1.80 (0.27), residues: 405 sheet: -0.75 (0.19), residues: 766 loop : -2.19 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 96 HIS 0.005 0.001 HIS A 374 PHE 0.028 0.001 PHE P 63 TYR 0.019 0.001 TYR P 91 ARG 0.002 0.000 ARG C 298 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 699) hydrogen bonds : angle 5.14403 ( 1815) SS BOND : bond 0.00489 ( 40) SS BOND : angle 1.63555 ( 80) covalent geometry : bond 0.00213 (21815) covalent geometry : angle 0.46209 (29603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8485 (p) cc_final: 0.8173 (t) REVERT: A 479 TRP cc_start: 0.7240 (m-10) cc_final: 0.6688 (m-10) REVERT: E 87 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6185 (tm-30) REVERT: C 96 TRP cc_start: 0.7060 (p90) cc_final: 0.6797 (p90) REVERT: C 475 MET cc_start: 0.8159 (tpp) cc_final: 0.7341 (tpp) REVERT: Q 27 GLN cc_start: 0.2321 (tm-30) cc_final: 0.1705 (tp40) outliers start: 29 outliers final: 22 residues processed: 261 average time/residue: 0.4775 time to fit residues: 195.4444 Evaluate side-chains 255 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 202 optimal weight: 9.9990 chunk 155 optimal weight: 0.0040 chunk 55 optimal weight: 0.5980 chunk 110 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 overall best weight: 1.5254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 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 = 0.4468 r_free = 0.4468 target = 0.166584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.147232 restraints weight = 85963.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.149092 restraints weight = 139236.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.149087 restraints weight = 58756.616| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21855 Z= 0.122 Angle : 0.496 13.524 29683 Z= 0.258 Chirality : 0.041 0.215 3310 Planarity : 0.003 0.032 3790 Dihedral : 4.087 29.431 2887 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.56 % Allowed : 15.19 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2666 helix: 1.72 (0.27), residues: 408 sheet: -0.74 (0.19), residues: 766 loop : -2.22 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 47 HIS 0.005 0.001 HIS A 66 PHE 0.024 0.001 PHE P 63 TYR 0.022 0.001 TYR P 91 ARG 0.004 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 699) hydrogen bonds : angle 5.14596 ( 1815) SS BOND : bond 0.00315 ( 40) SS BOND : angle 1.58360 ( 80) covalent geometry : bond 0.00288 (21815) covalent geometry : angle 0.48981 (29603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8472 (p) cc_final: 0.8195 (t) REVERT: A 479 TRP cc_start: 0.7237 (m-10) cc_final: 0.6663 (m-10) REVERT: E 87 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6263 (tm-30) REVERT: J 55 GLU cc_start: 0.4837 (OUTLIER) cc_final: 0.4570 (mm-30) REVERT: Q 27 GLN cc_start: 0.2272 (tm-30) cc_final: 0.1645 (tp40) outliers start: 37 outliers final: 29 residues processed: 262 average time/residue: 0.4085 time to fit residues: 168.3991 Evaluate side-chains 262 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain J residue 55 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 184 optimal weight: 0.4980 chunk 127 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 246 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 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 = 0.4473 r_free = 0.4473 target = 0.166948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.144097 restraints weight = 85897.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.147634 restraints weight = 149696.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.148205 restraints weight = 56114.325| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21855 Z= 0.112 Angle : 0.490 13.260 29683 Z= 0.254 Chirality : 0.041 0.235 3310 Planarity : 0.003 0.031 3790 Dihedral : 4.032 29.821 2887 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 33.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.65 % Allowed : 15.11 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2666 helix: 1.80 (0.27), residues: 408 sheet: -0.72 (0.19), residues: 772 loop : -2.20 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 96 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE I 100E TYR 0.024 0.001 TYR P 91 ARG 0.003 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 699) hydrogen bonds : angle 5.06458 ( 1815) SS BOND : bond 0.00307 ( 40) SS BOND : angle 1.55824 ( 80) covalent geometry : bond 0.00262 (21815) covalent geometry : angle 0.48365 (29603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 644 THR cc_start: 0.8411 (p) cc_final: 0.8136 (t) REVERT: Z 633 LYS cc_start: 0.7291 (pttt) cc_final: 0.6807 (ptmt) REVERT: A 479 TRP cc_start: 0.7387 (m-10) cc_final: 0.6835 (m-10) REVERT: E 87 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6261 (tm-30) REVERT: C 96 TRP cc_start: 0.7009 (p90) cc_final: 0.6780 (p90) REVERT: C 475 MET cc_start: 0.8209 (tpp) cc_final: 0.7359 (tpp) REVERT: Q 27 GLN cc_start: 0.2395 (tm-30) cc_final: 0.1766 (tp40) outliers start: 39 outliers final: 34 residues processed: 264 average time/residue: 0.3910 time to fit residues: 162.4043 Evaluate side-chains 267 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 648 VAL Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 151 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 143 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.0270 chunk 177 optimal weight: 30.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 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 = 0.4492 r_free = 0.4492 target = 0.168464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.146369 restraints weight = 85989.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.149698 restraints weight = 140772.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.149994 restraints weight = 54574.825| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 21855 Z= 0.087 Angle : 0.459 11.844 29683 Z= 0.238 Chirality : 0.040 0.227 3310 Planarity : 0.003 0.031 3790 Dihedral : 3.799 29.099 2887 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 32.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.22 % Allowed : 15.57 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2666 helix: 2.05 (0.27), residues: 405 sheet: -0.65 (0.19), residues: 778 loop : -2.12 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 103 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE I 100E TYR 0.026 0.001 TYR P 91 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 699) hydrogen bonds : angle 4.87080 ( 1815) SS BOND : bond 0.00280 ( 40) SS BOND : angle 1.43599 ( 80) covalent geometry : bond 0.00205 (21815) covalent geometry : angle 0.45363 (29603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 566 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7466 (mt) REVERT: Y 644 THR cc_start: 0.8515 (p) cc_final: 0.8186 (t) REVERT: Z 633 LYS cc_start: 0.7335 (pttt) cc_final: 0.6885 (ptmt) REVERT: A 479 TRP cc_start: 0.7297 (m-10) cc_final: 0.6684 (m-10) REVERT: E 87 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6251 (tm-30) REVERT: C 423 ILE cc_start: 0.5179 (OUTLIER) cc_final: 0.4839 (pt) REVERT: C 475 MET cc_start: 0.8095 (tpp) cc_final: 0.7271 (tpp) REVERT: I 51 PHE cc_start: 0.5835 (t80) cc_final: 0.5608 (t80) REVERT: Q 27 GLN cc_start: 0.2387 (tm-30) cc_final: 0.1274 (tp40) outliers start: 29 outliers final: 24 residues processed: 258 average time/residue: 0.4062 time to fit residues: 164.3823 Evaluate side-chains 258 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain I residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 236 optimal weight: 0.0870 chunk 253 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 170 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 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 = 0.4433 r_free = 0.4433 target = 0.163604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.140081 restraints weight = 85372.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.143546 restraints weight = 150813.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.144299 restraints weight = 56221.195| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21855 Z= 0.205 Angle : 0.588 11.844 29683 Z= 0.307 Chirality : 0.043 0.231 3310 Planarity : 0.004 0.033 3790 Dihedral : 4.500 32.167 2887 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 37.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 1.52 % Allowed : 15.44 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2666 helix: 1.47 (0.27), residues: 409 sheet: -0.83 (0.20), residues: 705 loop : -2.24 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 96 HIS 0.007 0.001 HIS A 66 PHE 0.019 0.002 PHE I 100E TYR 0.025 0.002 TYR P 91 ARG 0.005 0.000 ARG C 503 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 699) hydrogen bonds : angle 5.33547 ( 1815) SS BOND : bond 0.00424 ( 40) SS BOND : angle 1.63330 ( 80) covalent geometry : bond 0.00483 (21815) covalent geometry : angle 0.58265 (29603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8349.42 seconds wall clock time: 149 minutes 33.38 seconds (8973.38 seconds total)