Starting phenix.real_space_refine on Sat Nov 18 20:01:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/11_2023/6vks_21228_updated.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 137 5.16 5 C 15458 2.51 5 N 3920 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 719": "OE1" <-> "OE2" Residue "B GLU 855": "OE1" <-> "OE2" Residue "B PHE 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 24034 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 7864 Classifications: {'peptide': 1049} Link IDs: {'PTRANS': 40, 'TRANS': 1008} Chain: "B" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7788 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 40, 'TRANS': 999} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 201 Unusual residues: {'AIX': 1, 'PTY': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIX:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 274 Unusual residues: {'PTY': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 12.78, per 1000 atoms: 0.53 Number of scatterers: 24034 At special positions: 0 Unit cell: (123.2, 116.6, 147.4, 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 137 16.00 P 15 15.00 O 4504 8.00 N 3920 7.00 C 15458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 4.5 seconds 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 19 sheets defined 49.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.633A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.717A pdb=" N SER A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.681A pdb=" N TYR A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.077A pdb=" N ASN A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 328 through 357 removed outlier: 3.501A pdb=" N PHE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 383 removed outlier: 5.524A pdb=" N ILE A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 390 through 421 removed outlier: 3.828A pdb=" N PHE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 451 removed outlier: 5.607A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 462 through 493 removed outlier: 4.566A pdb=" N GLN A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 509 through 532 removed outlier: 4.185A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.558A pdb=" N ALA A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.618A pdb=" N GLY A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 689 through 703 Processing helix chain 'A' and resid 730 through 733 No H-bonds generated for 'chain 'A' and resid 730 through 733' Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 834 through 846 Processing helix chain 'A' and resid 858 through 863 removed outlier: 3.921A pdb=" N GLU A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 863 " --> pdb=" O SER A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 889 removed outlier: 4.135A pdb=" N ALA A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 3.796A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 894 through 898' Processing helix chain 'A' and resid 903 through 919 removed outlier: 4.175A pdb=" N LEU A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 957 removed outlier: 3.908A pdb=" N VAL A 937 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 989 removed outlier: 5.461A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 994 through 998 Processing helix chain 'A' and resid 1005 through 1040 removed outlier: 4.060A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A1029 " --> pdb=" O SER A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.940A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 removed outlier: 5.427A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 removed outlier: 3.964A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.655A pdb=" N GLN B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 125' Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 161 through 164 No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.949A pdb=" N ASN B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.571A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 356 removed outlier: 3.676A pdb=" N VAL B 331 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 332 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE B 333 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 341 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 344 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 353 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 356 " --> pdb=" O MET B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.649A pdb=" N ILE B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 390 through 398 Processing helix chain 'B' and resid 400 through 420 removed outlier: 3.790A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 456 removed outlier: 5.711A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Proline residue: B 453 - end of helix removed outlier: 4.133A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 493 removed outlier: 4.138A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 509 through 531 removed outlier: 3.556A pdb=" N PHE B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 554 Processing helix chain 'B' and resid 581 through 597 removed outlier: 3.866A pdb=" N SER B 597 " --> pdb=" O GLN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 653 removed outlier: 3.519A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 703 Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 741 through 750 Processing helix chain 'B' and resid 834 through 846 removed outlier: 3.921A pdb=" N GLU B 839 " --> pdb=" O GLY B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 863 removed outlier: 3.851A pdb=" N ARG B 861 " --> pdb=" O GLY B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 889 Processing helix chain 'B' and resid 894 through 900 removed outlier: 3.969A pdb=" N LEU B 900 " --> pdb=" O LEU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 922 removed outlier: 3.984A pdb=" N LEU B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 958 Processing helix chain 'B' and resid 967 through 997 removed outlier: 5.179A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1004 through 1039 removed outlier: 3.850A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.551A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.904A pdb=" N VAL C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 removed outlier: 3.828A pdb=" N GLN C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 125' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 198 through 207 Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.552A pdb=" N GLY C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 246' Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.716A pdb=" N ALA C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 357 removed outlier: 3.989A pdb=" N GLU C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 383 removed outlier: 4.144A pdb=" N VAL C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.566A pdb=" N GLU C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 425 through 435 removed outlier: 3.516A pdb=" N THR C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 455 removed outlier: 3.848A pdb=" N VAL C 450 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) Proline residue: C 453 - end of helix Processing helix chain 'C' and resid 459 through 493 removed outlier: 4.037A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 509 through 531 removed outlier: 3.525A pdb=" N GLY C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 581 through 595 Processing helix chain 'C' and resid 639 through 653 removed outlier: 3.515A pdb=" N LYS C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 702 Processing helix chain 'C' and resid 730 through 736 Processing helix chain 'C' and resid 740 through 749 Processing helix chain 'C' and resid 780 through 784 Processing helix chain 'C' and resid 798 through 801 No H-bonds generated for 'chain 'C' and resid 798 through 801' Processing helix chain 'C' and resid 834 through 845 Processing helix chain 'C' and resid 859 through 867 removed outlier: 4.078A pdb=" N GLY C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 888 Processing helix chain 'C' and resid 894 through 898 removed outlier: 3.760A pdb=" N VAL C 898 " --> pdb=" O ILE C 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 894 through 898' Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 933 through 961 removed outlier: 3.926A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 997 removed outlier: 3.845A pdb=" N GLU C 973 " --> pdb=" O GLU C 969 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.724A pdb=" N ALA C 988 " --> pdb=" O MET C 984 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1005 through 1039 removed outlier: 3.806A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix removed outlier: 4.013A pdb=" N VAL C1034 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.921A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 83 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.390A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.014A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.673A pdb=" N VAL A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 276 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 625 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 623 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR A 606 " --> pdb=" O MET A 621 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET A 621 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER A 608 " --> pdb=" O MET A 619 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET A 619 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 676 through 680 removed outlier: 4.249A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 826 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 721 through 725 Processing sheet with id= G, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.576A pdb=" N LEU A 137 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 289 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 139 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET A 287 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 172 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= I, first strand: chain 'B' and resid 138 through 140 removed outlier: 3.551A pdb=" N MET B 287 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 174 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= K, first strand: chain 'B' and resid 264 through 269 removed outlier: 9.278A pdb=" N MET B 182 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG B 767 " --> pdb=" O MET B 182 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE B 184 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET B 769 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL B 186 " --> pdb=" O MET B 769 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 276 through 279 removed outlier: 6.709A pdb=" N ILE B 625 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE B 623 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR B 606 " --> pdb=" O MET B 621 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET B 621 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER B 608 " --> pdb=" O MET B 619 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N MET B 619 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 570 " --> pdb=" O VAL B 662 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 721 through 723 Processing sheet with id= N, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.772A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 83 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 319 through 326 removed outlier: 7.293A pdb=" N ILE C 139 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET C 138 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 172 " --> pdb=" O MET C 290 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.430A pdb=" N LEU C 765 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N MET C 182 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 767 " --> pdb=" O MET C 182 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE C 184 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET C 769 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL C 186 " --> pdb=" O MET C 769 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN C 771 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 276 through 279 removed outlier: 6.704A pdb=" N ILE C 625 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE C 623 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR C 606 " --> pdb=" O MET C 621 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET C 621 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 573 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 676 through 681 Processing sheet with id= S, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.885A pdb=" N SER C 721 " --> pdb=" O GLY C 809 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 809 " --> pdb=" O SER C 721 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3327 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: 8.93 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3888 1.31 - 1.44: 6083 1.44 - 1.56: 14173 1.56 - 1.69: 32 1.69 - 1.81: 270 Bond restraints: 24446 Sorted by residual: bond pdb=" C8 PTY C1108 " pdb=" O10 PTY C1108 " ideal model delta sigma weight residual 1.205 1.451 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C6 AIX B1106 " pdb=" S1 AIX B1106 " ideal model delta sigma weight residual 1.693 1.474 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C13 AIX B1106 " pdb=" S1 AIX B1106 " ideal model delta sigma weight residual 1.464 1.654 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C8 PTY B1105 " pdb=" O7 PTY B1105 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C30 PTY B1105 " pdb=" O4 PTY B1105 " ideal model delta sigma weight residual 1.331 1.460 -0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 24441 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.49: 688 106.49 - 113.52: 13631 113.52 - 120.55: 9903 120.55 - 127.58: 8670 127.58 - 134.61: 155 Bond angle restraints: 33047 Sorted by residual: angle pdb=" O11 PTY B1104 " pdb=" P1 PTY B1104 " pdb=" O14 PTY B1104 " ideal model delta sigma weight residual 92.90 107.55 -14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O14 PTY B1101 " ideal model delta sigma weight residual 92.90 105.87 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" O11 PTY B1103 " pdb=" P1 PTY B1103 " pdb=" O14 PTY B1103 " ideal model delta sigma weight residual 92.90 105.63 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 PTY A1103 " pdb=" P1 PTY A1103 " pdb=" O14 PTY A1103 " ideal model delta sigma weight residual 92.90 105.58 -12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" O11 PTY C1103 " pdb=" P1 PTY C1103 " pdb=" O14 PTY C1103 " ideal model delta sigma weight residual 92.90 105.15 -12.25 3.00e+00 1.11e-01 1.67e+01 ... (remaining 33042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 14332 35.27 - 70.55: 234 70.55 - 105.82: 29 105.82 - 141.09: 8 141.09 - 176.36: 7 Dihedral angle restraints: 14610 sinusoidal: 5706 harmonic: 8904 Sorted by residual: dihedral pdb=" C3 PTY B1103 " pdb=" O11 PTY B1103 " pdb=" P1 PTY B1103 " pdb=" O12 PTY B1103 " ideal model delta sinusoidal sigma weight residual -59.77 116.59 -176.36 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY B1105 " pdb=" O11 PTY B1105 " pdb=" P1 PTY B1105 " pdb=" O12 PTY B1105 " ideal model delta sinusoidal sigma weight residual 300.23 124.45 175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N1 PTY B1101 " pdb=" C2 PTY B1101 " pdb=" C3 PTY B1101 " pdb=" O11 PTY B1101 " ideal model delta sinusoidal sigma weight residual 65.33 -128.71 -165.96 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 14607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3156 0.058 - 0.117: 592 0.117 - 0.175: 81 0.175 - 0.234: 16 0.234 - 0.292: 6 Chirality restraints: 3851 Sorted by residual: chirality pdb=" CA ASP C 97 " pdb=" N ASP C 97 " pdb=" C ASP C 97 " pdb=" CB ASP C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA LEU B 707 " pdb=" N LEU B 707 " pdb=" C LEU B 707 " pdb=" CB LEU B 707 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS B 507 " pdb=" N LYS B 507 " pdb=" C LYS B 507 " pdb=" CB LYS B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3848 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 902 " 0.069 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 903 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 903 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 903 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1046 " -0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLU A1046 " 0.073 2.00e-02 2.50e+03 pdb=" O GLU A1046 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A1047 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 861 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.86e+00 pdb=" NE ARG B 861 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 861 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 861 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 861 " -0.010 2.00e-02 2.50e+03 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 134 2.54 - 3.13: 16748 3.13 - 3.72: 35713 3.72 - 4.31: 49837 4.31 - 4.90: 84387 Nonbonded interactions: 186819 Sorted by model distance: nonbonded pdb=" O10 PTY A1103 " pdb=" O10 PTY C1104 " model vdw 1.946 3.040 nonbonded pdb=" O12 PTY C1102 " pdb=" O10 PTY C1107 " model vdw 2.053 3.040 nonbonded pdb=" NE2 GLN A 358 " pdb=" CE LYS A 507 " model vdw 2.065 3.520 nonbonded pdb=" OE1 GLN C 961 " pdb=" OH TYR C1033 " model vdw 2.188 2.440 nonbonded pdb=" NE2 GLN A 358 " pdb=" CD LYS A 507 " model vdw 2.232 3.520 ... (remaining 186814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1040 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1040 or (resid 1104 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 1040 or resid 1107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.350 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 65.580 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 24446 Z= 0.415 Angle : 0.890 14.651 33047 Z= 0.462 Chirality : 0.048 0.292 3851 Planarity : 0.008 0.120 4158 Dihedral : 15.048 176.364 8906 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.11), residues: 3125 helix: -2.47 (0.09), residues: 1532 sheet: -1.98 (0.24), residues: 402 loop : -2.69 (0.14), residues: 1191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.3629 time to fit residues: 308.9678 Evaluate side-chains 347 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.0030 chunk 236 optimal weight: 0.0010 chunk 131 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 283 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 211 GLN A 226 GLN A 280 ASN A 358 GLN A 574 GLN A 617 GLN A 762 GLN B 109 ASN B 147 GLN B 463 ASN B 593 GLN B 672 ASN B 761 ASN B 859 GLN B 917 ASN B 936 GLN B1007 GLN C 55 GLN C 101 ASN C 157 GLN C 179 GLN C 252 ASN C 283 ASN C 293 ASN C 566 GLN C 617 GLN C 681 GLN C 685 ASN C 696 ASN C 762 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN C 859 GLN C 936 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24446 Z= 0.144 Angle : 0.512 8.291 33047 Z= 0.256 Chirality : 0.040 0.221 3851 Planarity : 0.005 0.085 4158 Dihedral : 12.283 179.175 3658 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.24 % Allowed : 10.57 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3125 helix: -0.38 (0.12), residues: 1572 sheet: -1.57 (0.24), residues: 426 loop : -2.26 (0.15), residues: 1127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 373 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 394 average time/residue: 0.3346 time to fit residues: 216.8176 Evaluate side-chains 339 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 326 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2202 time to fit residues: 9.1007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN A 949 ASN B 672 ASN B 761 ASN C 101 ASN C 108 GLN C 681 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24446 Z= 0.288 Angle : 0.573 11.801 33047 Z= 0.289 Chirality : 0.043 0.205 3851 Planarity : 0.004 0.054 4158 Dihedral : 11.006 170.436 3658 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.72 % Allowed : 12.73 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3125 helix: 0.46 (0.13), residues: 1587 sheet: -1.27 (0.25), residues: 444 loop : -1.98 (0.17), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 357 average time/residue: 0.3511 time to fit residues: 205.6365 Evaluate side-chains 313 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 295 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2516 time to fit residues: 11.9629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 1.9990 chunk 213 optimal weight: 0.0010 chunk 147 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 135 optimal weight: 0.0040 chunk 190 optimal weight: 9.9990 chunk 284 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 790 ASN B 672 ASN C 101 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24446 Z= 0.128 Angle : 0.472 9.609 33047 Z= 0.239 Chirality : 0.039 0.171 3851 Planarity : 0.003 0.048 4158 Dihedral : 10.123 169.946 3658 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.20 % Allowed : 14.53 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3125 helix: 0.99 (0.14), residues: 1577 sheet: -0.99 (0.26), residues: 418 loop : -1.75 (0.17), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 306 time to evaluate : 2.851 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 327 average time/residue: 0.3165 time to fit residues: 170.0037 Evaluate side-chains 309 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 293 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2128 time to fit residues: 9.7746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 1.9990 chunk 171 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 224 optimal weight: 0.7980 chunk 124 optimal weight: 0.1980 chunk 257 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN B 672 ASN C 101 ASN C 790 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24446 Z= 0.140 Angle : 0.467 9.532 33047 Z= 0.236 Chirality : 0.039 0.140 3851 Planarity : 0.003 0.047 4158 Dihedral : 9.513 171.571 3658 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.44 % Allowed : 14.96 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3125 helix: 1.26 (0.14), residues: 1577 sheet: -0.75 (0.26), residues: 421 loop : -1.62 (0.17), residues: 1127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 307 time to evaluate : 2.869 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 325 average time/residue: 0.3369 time to fit residues: 182.0291 Evaluate side-chains 311 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 294 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2267 time to fit residues: 10.6283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.8980 chunk 271 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 301 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 672 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24446 Z= 0.154 Angle : 0.470 8.620 33047 Z= 0.238 Chirality : 0.040 0.141 3851 Planarity : 0.003 0.046 4158 Dihedral : 9.036 170.250 3658 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.96 % Allowed : 16.24 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 3125 helix: 1.43 (0.14), residues: 1571 sheet: -0.73 (0.26), residues: 422 loop : -1.42 (0.18), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 3.012 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 319 average time/residue: 0.3357 time to fit residues: 178.3744 Evaluate side-chains 308 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 298 time to evaluate : 2.889 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2645 time to fit residues: 8.5905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 171 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24446 Z= 0.199 Angle : 0.501 11.732 33047 Z= 0.253 Chirality : 0.041 0.145 3851 Planarity : 0.003 0.048 4158 Dihedral : 8.706 168.977 3658 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.04 % Allowed : 16.48 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 3125 helix: 1.45 (0.14), residues: 1592 sheet: -0.76 (0.27), residues: 411 loop : -1.37 (0.18), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 300 time to evaluate : 3.077 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 314 average time/residue: 0.3310 time to fit residues: 171.6388 Evaluate side-chains 312 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 293 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2178 time to fit residues: 11.2400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 4.9990 chunk 120 optimal weight: 0.0040 chunk 179 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 191 optimal weight: 0.0870 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN B 672 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24446 Z= 0.126 Angle : 0.469 10.928 33047 Z= 0.236 Chirality : 0.039 0.148 3851 Planarity : 0.003 0.044 4158 Dihedral : 8.329 167.667 3658 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.44 % Allowed : 17.12 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 3125 helix: 1.60 (0.14), residues: 1591 sheet: -0.70 (0.27), residues: 399 loop : -1.26 (0.18), residues: 1135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 316 time to evaluate : 2.807 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 320 average time/residue: 0.3442 time to fit residues: 181.5184 Evaluate side-chains 306 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 300 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2453 time to fit residues: 6.6003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 279 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS B 672 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24446 Z= 0.163 Angle : 0.486 10.822 33047 Z= 0.244 Chirality : 0.040 0.172 3851 Planarity : 0.003 0.044 4158 Dihedral : 8.179 167.619 3658 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.52 % Allowed : 17.60 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 3125 helix: 1.63 (0.14), residues: 1590 sheet: -0.67 (0.27), residues: 416 loop : -1.20 (0.18), residues: 1119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 301 time to evaluate : 2.638 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 309 average time/residue: 0.3298 time to fit residues: 168.9843 Evaluate side-chains 299 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 292 time to evaluate : 2.665 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4487 time to fit residues: 9.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 310 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 211 GLN B 672 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24446 Z= 0.220 Angle : 0.525 10.700 33047 Z= 0.264 Chirality : 0.041 0.141 3851 Planarity : 0.003 0.046 4158 Dihedral : 8.157 166.783 3658 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.20 % Allowed : 18.12 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 3125 helix: 1.51 (0.13), residues: 1603 sheet: -0.59 (0.27), residues: 418 loop : -1.22 (0.18), residues: 1104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 304 time to evaluate : 2.567 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 306 average time/residue: 0.3383 time to fit residues: 170.5834 Evaluate side-chains 294 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 292 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2492 time to fit residues: 4.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 413 ASN B 672 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 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 = 0.3615 r_free = 0.3615 target = 0.113362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096408 restraints weight = 40813.463| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.37 r_work: 0.3240 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24446 Z= 0.158 Angle : 0.501 10.879 33047 Z= 0.250 Chirality : 0.040 0.144 3851 Planarity : 0.003 0.045 4158 Dihedral : 7.959 166.212 3658 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.16 % Allowed : 18.48 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 3125 helix: 1.61 (0.14), residues: 1598 sheet: -0.67 (0.27), residues: 416 loop : -1.13 (0.18), residues: 1111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.79 seconds wall clock time: 97 minutes 7.29 seconds (5827.29 seconds total)