Starting phenix.real_space_refine on Thu Mar 5 22:25:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d5c_27208/03_2026/8d5c_27208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d5c_27208/03_2026/8d5c_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_27208/03_2026/8d5c_27208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d5c_27208/03_2026/8d5c_27208.map" model { file = "/net/cci-nas-00/data/ceres_data/8d5c_27208/03_2026/8d5c_27208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d5c_27208/03_2026/8d5c_27208.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.14, per 1000 atoms: 0.20 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: 1.91 Conformation dependent library (CDL) restraints added in 965.4 milliseconds 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: 0.81 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: 5.18 Time building geometry restraints manager: 2.75 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.510 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 : 32.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG L 18 TYR 0.015 0.001 TYR H 97 PHE 0.049 0.001 PHE H 51 TRP 0.038 0.001 TRP H 33 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00202 (21815) covalent geometry : angle 0.47587 (29603) SS BOND : bond 0.00338 ( 40) SS BOND : angle 0.99311 ( 80) hydrogen bonds : bond 0.17680 ( 699) hydrogen bonds : angle 6.47612 ( 1815) *********************** 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 : 0.896 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: 0.6093 (t70) REVERT: E 87 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6133 (tm-30) REVERT: F 14 LEU cc_start: 0.5947 (mm) cc_final: 0.5554 (mm) REVERT: F 70 ILE cc_start: 0.6836 (mm) cc_final: 0.6530 (mm) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1814 time to fit residues: 88.9532 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 : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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** ** Z 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 616 ASN Z 658 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN A 462 GLN ** 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 C 478 ASN F 89 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.171349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.149211 restraints weight = 86583.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.152292 restraints weight = 134393.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.152011 restraints weight = 54493.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.152810 restraints weight = 43190.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.153067 restraints weight = 33634.429| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21855 Z= 0.101 Angle : 0.471 6.331 29683 Z= 0.249 Chirality : 0.041 0.140 3310 Planarity : 0.003 0.037 3790 Dihedral : 3.852 31.792 2887 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.55 % Allowed : 5.82 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2666 helix: 1.47 (0.27), residues: 423 sheet: -0.73 (0.19), residues: 768 loop : -2.14 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 61 TYR 0.016 0.001 TYR H 97 PHE 0.021 0.001 PHE H 51 TRP 0.021 0.001 TRP C 96 HIS 0.010 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00225 (21815) covalent geometry : angle 0.46789 (29603) SS BOND : bond 0.00351 ( 40) SS BOND : angle 1.13607 ( 80) hydrogen bonds : bond 0.03917 ( 699) hydrogen bonds : angle 5.57458 ( 1815) *********************** 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 268 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 0.801 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: X 537 LEU cc_start: 0.6460 (tp) cc_final: 0.6239 (tt) REVERT: Y 584 GLU cc_start: 0.8035 (tp30) cc_final: 0.7803 (tp30) REVERT: Y 644 THR cc_start: 0.8423 (p) cc_final: 0.8102 (t) REVERT: Z 589 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7297 (t0) REVERT: A 475 MET cc_start: 0.7658 (mmm) cc_final: 0.7403 (mmp) REVERT: E 87 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6071 (tm-30) REVERT: F 28 TRP cc_start: 0.4784 (m100) cc_final: 0.4410 (m100) outliers start: 13 outliers final: 9 residues processed: 263 average time/residue: 0.1736 time to fit residues: 72.5562 Evaluate side-chains 245 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 648 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 293 GLU Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 24 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 89 optimal weight: 0.0570 chunk 159 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 overall best weight: 3.3504 ------------------------------------------------------------------------------- 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 103 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN 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 82 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.164841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.143669 restraints weight = 86696.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.146365 restraints weight = 145599.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.146525 restraints weight = 58341.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.147107 restraints weight = 44599.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.147398 restraints weight = 35343.631| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21855 Z= 0.231 Angle : 0.624 9.859 29683 Z= 0.327 Chirality : 0.044 0.173 3310 Planarity : 0.004 0.039 3790 Dihedral : 4.612 33.304 2887 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 37.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 1.56 % Allowed : 10.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.16), residues: 2666 helix: 0.84 (0.26), residues: 426 sheet: -0.92 (0.20), residues: 696 loop : -2.29 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 503 TYR 0.022 0.002 TYR H 97 PHE 0.021 0.002 PHE B 53 TRP 0.027 0.002 TRP B 112 HIS 0.009 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00539 (21815) covalent geometry : angle 0.61892 (29603) SS BOND : bond 0.00637 ( 40) SS BOND : angle 1.69688 ( 80) hydrogen bonds : bond 0.05375 ( 699) hydrogen bonds : angle 5.89271 ( 1815) *********************** 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 277 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.952 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: 0.8395 (p) cc_final: 0.8122 (t) REVERT: Z 589 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7492 (t0) REVERT: E 87 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6212 (tm-30) outliers start: 37 outliers final: 26 residues processed: 263 average time/residue: 0.1795 time to fit residues: 74.9097 Evaluate side-chains 256 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 0.9980 chunk 141 optimal weight: 40.0000 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 261 optimal weight: 30.0000 chunk 249 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** 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 = 0.4490 r_free = 0.4490 target = 0.168355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.146000 restraints weight = 85800.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.149357 restraints weight = 140868.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.148975 restraints weight = 55015.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.149293 restraints weight = 56545.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.150098 restraints weight = 36918.438| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 21855 Z= 0.097 Angle : 0.472 12.160 29683 Z= 0.247 Chirality : 0.041 0.221 3310 Planarity : 0.003 0.035 3790 Dihedral : 4.127 31.316 2887 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.22 % Allowed : 11.39 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.16), residues: 2666 helix: 1.63 (0.27), residues: 405 sheet: -0.84 (0.20), residues: 700 loop : -2.14 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 503 TYR 0.019 0.001 TYR H 97 PHE 0.011 0.001 PHE H 51 TRP 0.019 0.001 TRP C 96 HIS 0.006 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00223 (21815) covalent geometry : angle 0.46447 (29603) SS BOND : bond 0.00477 ( 40) SS BOND : angle 1.64911 ( 80) hydrogen bonds : bond 0.03803 ( 699) hydrogen bonds : angle 5.41363 ( 1815) *********************** 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 266 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.800 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: 0.8343 (p) cc_final: 0.8055 (t) REVERT: Z 589 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7606 (t0) REVERT: A 475 MET cc_start: 0.7643 (mmm) cc_final: 0.7327 (mmp) REVERT: E 87 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6110 (tm-30) REVERT: C 96 TRP cc_start: 0.6930 (p90) cc_final: 0.6687 (p90) REVERT: C 475 MET cc_start: 0.7996 (tpp) cc_final: 0.7274 (tpp) REVERT: Q 27 GLN cc_start: 0.1537 (tm-30) cc_final: 0.1053 (tp40) outliers start: 29 outliers final: 20 residues processed: 258 average time/residue: 0.1772 time to fit residues: 72.4453 Evaluate side-chains 249 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 Z residue 589 ASP Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 428 GLN 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 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 Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 252 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 119 optimal weight: 0.0570 chunk 236 optimal weight: 0.2980 chunk 150 optimal weight: 5.9990 chunk 67 optimal weight: 0.0070 chunk 32 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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** ** 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 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.170150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.148269 restraints weight = 85763.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.151356 restraints weight = 136406.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.151317 restraints weight = 53166.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.151941 restraints weight = 42902.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.152235 restraints weight = 33482.283| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 21855 Z= 0.082 Angle : 0.447 12.057 29683 Z= 0.232 Chirality : 0.040 0.258 3310 Planarity : 0.003 0.036 3790 Dihedral : 3.763 28.807 2887 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 30.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.97 % Allowed : 12.62 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2666 helix: 1.94 (0.27), residues: 405 sheet: -0.68 (0.19), residues: 768 loop : -2.08 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 94 TYR 0.015 0.001 TYR H 97 PHE 0.027 0.001 PHE P 63 TRP 0.012 0.001 TRP H 33 HIS 0.005 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00191 (21815) covalent geometry : angle 0.43970 (29603) SS BOND : bond 0.00322 ( 40) SS BOND : angle 1.56925 ( 80) hydrogen bonds : bond 0.03082 ( 699) hydrogen bonds : angle 5.10884 ( 1815) *********************** 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 267 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.735 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: X 537 LEU cc_start: 0.6318 (tp) cc_final: 0.6057 (tt) REVERT: Y 644 THR cc_start: 0.8433 (p) cc_final: 0.8140 (t) REVERT: Z 589 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7490 (t0) REVERT: A 475 MET cc_start: 0.7587 (mmm) cc_final: 0.7382 (mmt) REVERT: E 87 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6135 (tm-30) REVERT: C 475 MET cc_start: 0.8030 (tpp) cc_final: 0.7316 (tpp) REVERT: Q 27 GLN cc_start: 0.1518 (tm-30) cc_final: 0.0996 (tp40) outliers start: 23 outliers final: 18 residues processed: 260 average time/residue: 0.1771 time to fit residues: 72.7504 Evaluate side-chains 245 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 548 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP 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 A residue 125 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain C residue 100 MET 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 I residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 0.0030 chunk 167 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 179 optimal weight: 0.0010 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 462 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.170173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.147548 restraints weight = 85268.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.150867 restraints weight = 133668.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.150824 restraints weight = 51462.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.151543 restraints weight = 41272.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.151813 restraints weight = 33097.569| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 21855 Z= 0.082 Angle : 0.439 6.471 29683 Z= 0.228 Chirality : 0.040 0.185 3310 Planarity : 0.003 0.032 3790 Dihedral : 3.677 28.267 2887 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 30.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.35 % Favored : 92.61 % Rotamer: Outliers : 1.18 % Allowed : 12.87 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.16), residues: 2666 helix: 2.09 (0.27), residues: 405 sheet: -0.60 (0.19), residues: 768 loop : -2.05 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 298 TYR 0.014 0.001 TYR H 97 PHE 0.034 0.001 PHE P 63 TRP 0.025 0.001 TRP C 96 HIS 0.004 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00195 (21815) covalent geometry : angle 0.43355 (29603) SS BOND : bond 0.00394 ( 40) SS BOND : angle 1.40068 ( 80) hydrogen bonds : bond 0.03035 ( 699) hydrogen bonds : angle 4.97493 ( 1815) *********************** 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 263 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.818 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: X 537 LEU cc_start: 0.6238 (tp) cc_final: 0.5957 (tt) REVERT: Y 644 THR cc_start: 0.8468 (p) cc_final: 0.8167 (t) REVERT: Z 589 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7480 (t0) REVERT: A 475 MET cc_start: 0.7716 (mmm) cc_final: 0.7020 (mmt) REVERT: E 87 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6130 (tm-30) REVERT: C 96 TRP cc_start: 0.6982 (p90) cc_final: 0.6749 (p90) REVERT: C 475 MET cc_start: 0.8063 (tpp) cc_final: 0.7308 (tpp) REVERT: Q 27 GLN cc_start: 0.1560 (tm-30) cc_final: 0.1166 (tp40) outliers start: 28 outliers final: 21 residues processed: 255 average time/residue: 0.1675 time to fit residues: 68.5362 Evaluate side-chains 251 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 Y residue 548 ILE Chi-restraints excluded: chain Z residue 568 LEU Chi-restraints excluded: chain Z residue 589 ASP 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 A residue 122 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 428 GLN 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 16 CYS Chi-restraints excluded: chain E residue 24 ILE 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 424 ILE Chi-restraints excluded: chain H residue 63 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 5.9990 chunk 191 optimal weight: 0.0470 chunk 107 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- 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** ** 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** P 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.166950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.144713 restraints weight = 85597.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.148127 restraints weight = 146598.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.148294 restraints weight = 55964.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.148905 restraints weight = 44653.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.149169 restraints weight = 35235.179| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21855 Z= 0.146 Angle : 0.506 10.500 29683 Z= 0.264 Chirality : 0.042 0.285 3310 Planarity : 0.003 0.034 3790 Dihedral : 4.010 29.978 2887 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 33.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 1.90 % Allowed : 12.91 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.16), residues: 2666 helix: 1.84 (0.27), residues: 408 sheet: -0.65 (0.19), residues: 762 loop : -2.13 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 59 TYR 0.018 0.001 TYR H 97 PHE 0.024 0.002 PHE P 63 TRP 0.014 0.001 TRP B 479 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00343 (21815) covalent geometry : angle 0.49984 (29603) SS BOND : bond 0.00515 ( 40) SS BOND : angle 1.61532 ( 80) hydrogen bonds : bond 0.03929 ( 699) hydrogen bonds : angle 5.15611 ( 1815) *********************** 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 276 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.717 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: Y 644 THR cc_start: 0.8376 (p) cc_final: 0.8094 (t) REVERT: A 479 TRP cc_start: 0.7132 (m-10) cc_final: 0.6851 (m-10) REVERT: E 87 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6252 (tm-30) REVERT: C 475 MET cc_start: 0.8209 (tpp) cc_final: 0.7443 (tpp) REVERT: L 45 LYS cc_start: 0.8622 (mptt) cc_final: 0.8323 (tttp) REVERT: Q 27 GLN cc_start: 0.1707 (tm-30) cc_final: 0.1004 (tp40) outliers start: 45 outliers final: 33 residues processed: 260 average time/residue: 0.1740 time to fit residues: 72.7068 Evaluate side-chains 261 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 566 LEU 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 Z residue 619 ILE 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 122 LEU Chi-restraints excluded: chain A residue 428 GLN 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 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 97 VAL 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 H residue 63 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 63 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** A 478 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 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 ** J 89 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 = 0.4404 r_free = 0.4404 target = 0.161251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.141585 restraints weight = 86655.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.143268 restraints weight = 146775.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.143603 restraints weight = 60522.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.143639 restraints weight = 55453.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.144293 restraints weight = 39041.673| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21855 Z= 0.301 Angle : 0.731 13.892 29683 Z= 0.384 Chirality : 0.047 0.245 3310 Planarity : 0.005 0.049 3790 Dihedral : 5.231 34.971 2887 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 42.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 2.32 % Allowed : 13.33 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 2666 helix: 0.74 (0.26), residues: 414 sheet: -0.95 (0.20), residues: 675 loop : -2.52 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 59 TYR 0.023 0.003 TYR H 97 PHE 0.025 0.003 PHE A 53 TRP 0.030 0.003 TRP C 395 HIS 0.009 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00704 (21815) covalent geometry : angle 0.72510 (29603) SS BOND : bond 0.00568 ( 40) SS BOND : angle 1.94204 ( 80) hydrogen bonds : bond 0.06118 ( 699) hydrogen bonds : angle 5.91740 ( 1815) *********************** 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 280 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.874 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: 0.8369 (p) cc_final: 0.8107 (t) REVERT: Z 633 LYS cc_start: 0.7330 (pttt) cc_final: 0.6851 (ptmt) REVERT: D 166 LYS cc_start: 0.7710 (mmtt) cc_final: 0.6998 (tttm) REVERT: C 475 MET cc_start: 0.8463 (tpp) cc_final: 0.7750 (tpp) outliers start: 55 outliers final: 42 residues processed: 259 average time/residue: 0.1779 time to fit residues: 72.9400 Evaluate side-chains 262 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 566 LEU 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 122 LEU 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 414 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 15 THR 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 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 F residue 106 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain Q residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 34 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 138 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- 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 428 GLN ** 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** E 129 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.163534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.136839 restraints weight = 85960.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.134963 restraints weight = 99510.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.131837 restraints weight = 72165.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.132530 restraints weight = 65402.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.132671 restraints weight = 53391.255| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21855 Z= 0.178 Angle : 0.572 13.784 29683 Z= 0.300 Chirality : 0.043 0.239 3310 Planarity : 0.004 0.073 3790 Dihedral : 4.798 34.863 2887 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 37.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 1.43 % Allowed : 14.68 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.16), residues: 2666 helix: 1.08 (0.26), residues: 409 sheet: -0.95 (0.20), residues: 683 loop : -2.45 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 503 TYR 0.023 0.002 TYR H 97 PHE 0.015 0.002 PHE A 53 TRP 0.022 0.002 TRP C 96 HIS 0.010 0.001 HIS X 564 Details of bonding type rmsd covalent geometry : bond 0.00416 (21815) covalent geometry : angle 0.56563 (29603) SS BOND : bond 0.00411 ( 40) SS BOND : angle 1.70906 ( 80) hydrogen bonds : bond 0.04730 ( 699) hydrogen bonds : angle 5.56138 ( 1815) *********************** 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 269 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.759 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: Y 644 THR cc_start: 0.8607 (p) cc_final: 0.8310 (t) REVERT: Z 633 LYS cc_start: 0.7457 (pttt) cc_final: 0.7007 (ptmt) REVERT: A 479 TRP cc_start: 0.7374 (m-10) cc_final: 0.7052 (m-10) REVERT: D 166 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7039 (tttm) REVERT: C 96 TRP cc_start: 0.7118 (p90) cc_final: 0.6832 (p90) REVERT: C 294 ILE cc_start: 0.5680 (tt) cc_final: 0.5269 (tt) REVERT: C 475 MET cc_start: 0.8330 (tpp) cc_final: 0.7454 (tpp) REVERT: H 105 GLN cc_start: 0.8688 (pp30) cc_final: 0.8480 (pp30) REVERT: J 49 TYR cc_start: 0.6155 (p90) cc_final: 0.4448 (p90) REVERT: P 40 ARG cc_start: 0.6647 (ttp80) cc_final: 0.5725 (mtp-110) REVERT: Q 27 GLN cc_start: 0.2241 (tm-30) cc_final: 0.1551 (tp-100) outliers start: 34 outliers final: 34 residues processed: 256 average time/residue: 0.1784 time to fit residues: 72.5579 Evaluate side-chains 265 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 566 LEU 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 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 96 LEU 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 505 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain Q residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 97 optimal weight: 0.3980 chunk 129 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 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 = 0.4472 r_free = 0.4472 target = 0.166963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.143026 restraints weight = 85565.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.146823 restraints weight = 146409.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.147697 restraints weight = 54162.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.148307 restraints weight = 42501.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.148549 restraints weight = 33413.591| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2816 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= 0.095 Angle : 0.483 12.085 29683 Z= 0.251 Chirality : 0.041 0.231 3310 Planarity : 0.003 0.032 3790 Dihedral : 4.152 31.080 2887 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 33.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.10 % Allowed : 14.94 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2666 helix: 1.76 (0.27), residues: 402 sheet: -0.91 (0.19), residues: 787 loop : -2.29 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.016 0.001 TYR H 97 PHE 0.013 0.001 PHE I 51 TRP 0.018 0.001 TRP H 33 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00222 (21815) covalent geometry : angle 0.47747 (29603) SS BOND : bond 0.00300 ( 40) SS BOND : angle 1.46098 ( 80) hydrogen bonds : bond 0.03388 ( 699) hydrogen bonds : angle 5.10292 ( 1815) ********************** 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 268 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.876 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: Y 644 THR cc_start: 0.8375 (p) cc_final: 0.8074 (t) REVERT: Z 633 LYS cc_start: 0.7364 (pttt) cc_final: 0.6881 (ptmt) REVERT: D 166 LYS cc_start: 0.7615 (mmtt) cc_final: 0.6790 (tttm) REVERT: E 87 GLU cc_start: 0.6626 (tm-30) cc_final: 0.6313 (tm-30) REVERT: J 49 TYR cc_start: 0.6080 (p90) cc_final: 0.4238 (p90) REVERT: P 91 TYR cc_start: 0.5951 (m-80) cc_final: 0.5635 (m-10) outliers start: 26 outliers final: 24 residues processed: 260 average time/residue: 0.1835 time to fit residues: 75.2876 Evaluate side-chains 255 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 THR 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 24 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 95 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 208 optimal weight: 0.0970 chunk 227 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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** ** C 280 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.164989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.140963 restraints weight = 85506.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.145031 restraints weight = 147407.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.145435 restraints weight = 54912.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.146195 restraints weight = 42986.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.146487 restraints weight = 34031.405| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2945 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= 0.147 Angle : 0.525 11.845 29683 Z= 0.274 Chirality : 0.042 0.222 3310 Planarity : 0.003 0.033 3790 Dihedral : 4.292 31.152 2887 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 35.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 1.39 % Allowed : 14.94 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.16), residues: 2666 helix: 1.59 (0.27), residues: 409 sheet: -0.84 (0.19), residues: 771 loop : -2.35 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 503 TYR 0.019 0.001 TYR H 97 PHE 0.027 0.002 PHE I 100E TRP 0.028 0.001 TRP C 96 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00345 (21815) covalent geometry : angle 0.52017 (29603) SS BOND : bond 0.00348 ( 40) SS BOND : angle 1.50284 ( 80) hydrogen bonds : bond 0.03940 ( 699) hydrogen bonds : angle 5.19712 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3780.98 seconds wall clock time: 66 minutes 10.38 seconds (3970.38 seconds total)