Starting phenix.real_space_refine on Mon Feb 19 05:58:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/02_2024/7rr6_24653_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/02_2024/7rr6_24653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/02_2024/7rr6_24653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/02_2024/7rr6_24653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/02_2024/7rr6_24653_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/02_2024/7rr6_24653_updated.pdb" } resolution = 3.1 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= 0.019 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 132 5.16 5 C 15413 2.51 5 N 3824 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 947": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23821 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7756 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 976} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7752 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 976} 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: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7658 Classifications: {'peptide': 1019} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 197 Unusual residues: {'D12': 4, 'PTY': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PTY:plan-1': 5, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Unusual residues: {'D12': 4, 'PTY': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-1': 2, 'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Unusual residues: {'PTY': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PTY:plan-1': 5, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 11.37, per 1000 atoms: 0.48 Number of scatterers: 23821 At special positions: 0 Unit cell: (121.049, 115.124, 145.598, 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 132 16.00 P 15 15.00 O 4437 8.00 N 3824 7.00 C 15413 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=0, symmetry=0 Time building additional restraints: 8.56 Conformation dependent library (CDL) restraints added in 3.8 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 24 sheets defined 51.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 100 through 117 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.508A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.685A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.336A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.141A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 456 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.610A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.577A pdb=" N ARG B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 557 removed outlier: 3.797A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 600 Processing helix chain 'B' and resid 644 through 657 removed outlier: 4.236A pdb=" N GLN B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 708 removed outlier: 3.684A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 743 through 754 Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 837 through 849 removed outlier: 4.048A pdb=" N SER B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'B' and resid 873 through 892 Processing helix chain 'B' and resid 897 through 902 removed outlier: 3.687A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 919 removed outlier: 3.778A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 955 Processing helix chain 'B' and resid 960 through 990 removed outlier: 4.005A pdb=" N LEU B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix removed outlier: 4.254A pdb=" N LEU B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 997 through 1013 removed outlier: 4.257A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1032 Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.682A pdb=" N GLY C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 100 through 111 removed outlier: 3.616A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.800A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.714A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.978A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'C' and resid 402 through 422 removed outlier: 4.260A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.772A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 Processing helix chain 'C' and resid 517 through 536 removed outlier: 3.616A pdb=" N LEU C 535 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG C 536 " --> pdb=" O GLY C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 558 Processing helix chain 'C' and resid 584 through 600 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 644 through 657 removed outlier: 4.140A pdb=" N GLN C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 707 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 743 through 754 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 783 through 788 removed outlier: 3.582A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 837 through 849 Processing helix chain 'C' and resid 861 through 892 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 905 through 919 removed outlier: 4.040A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 954 removed outlier: 3.568A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 970 Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.873A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 1000 through 1013 removed outlier: 4.056A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 Proline residue: C1023 - end of helix Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 62 through 65 No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.834A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 299 through 316 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.903A pdb=" N VAL A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 386 removed outlier: 3.762A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 403 through 423 removed outlier: 4.671A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 449 removed outlier: 3.702A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 463 through 495 removed outlier: 3.617A pdb=" N SER A 476 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A 488 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.994A pdb=" N CYS A 493 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.691A pdb=" N LEU A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 546 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 600 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 692 through 707 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 841 through 847 removed outlier: 3.616A pdb=" N MET A 844 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 847 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 868 removed outlier: 3.656A pdb=" N LEU A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.563A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 3.938A pdb=" N ALA A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 953 removed outlier: 3.515A pdb=" N THR A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 973 through 991 removed outlier: 3.565A pdb=" N VAL A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 997 through 1016 removed outlier: 3.567A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 Processing sheet with id= A, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.556A pdb=" N ALA B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 81 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 144 Processing sheet with id= C, first strand: chain 'B' and resid 175 through 177 Processing sheet with id= D, first strand: chain 'B' and resid 266 through 268 removed outlier: 9.259A pdb=" N MET B 184 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS B 770 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE B 186 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 772 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET B 188 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET B 774 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.734A pdb=" N SER B 608 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 679 through 683 Processing sheet with id= G, first strand: chain 'B' and resid 724 through 731 Processing sheet with id= H, first strand: chain 'B' and resid 790 through 792 Processing sheet with id= I, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.620A pdb=" N SER C 46 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 322 through 324 removed outlier: 7.111A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C 289 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY C 141 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER C 287 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE C 143 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER C 630 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 609 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE C 628 " --> pdb=" O VAL C 609 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA C 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 626 " --> pdb=" O ALA C 611 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 613 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR C 624 " --> pdb=" O ASN C 613 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 574 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.208A pdb=" N TYR C 182 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS C 770 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.160A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 824 through 827 Processing sheet with id= N, first strand: chain 'C' and resid 723 through 731 Processing sheet with id= O, first strand: chain 'C' and resid 790 through 792 Processing sheet with id= P, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.037A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.545A pdb=" N ALA A 47 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.364A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 321 through 324 Processing sheet with id= S, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.650A pdb=" N VAL A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N MET A 184 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS A 770 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE A 186 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR A 772 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET A 188 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET A 774 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 284 through 286 removed outlier: 4.144A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER A 630 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 609 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 628 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 611 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 626 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN A 613 " --> pdb=" O THR A 624 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR A 624 " --> pdb=" O ASN A 613 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 627 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 717 through 719 removed outlier: 4.318A pdb=" N GLU A 826 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 724 through 731 Processing sheet with id= W, first strand: chain 'A' and resid 790 through 792 Processing sheet with id= X, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.062A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.40 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3888 1.30 - 1.44: 5859 1.44 - 1.57: 14181 1.57 - 1.70: 30 1.70 - 1.83: 258 Bond restraints: 24216 Sorted by residual: bond pdb=" C ARG B 973 " pdb=" O ARG B 973 " ideal model delta sigma weight residual 1.244 1.185 0.058 1.00e-02 1.00e+04 3.38e+01 bond pdb=" N PRO B 318 " pdb=" CD PRO B 318 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.31e+01 bond pdb=" C GLU C 130 " pdb=" N LYS C 131 " ideal model delta sigma weight residual 1.330 1.393 -0.063 1.32e-02 5.74e+03 2.30e+01 bond pdb=" C GLY C 998 " pdb=" O GLY C 998 " ideal model delta sigma weight residual 1.233 1.286 -0.053 1.13e-02 7.83e+03 2.21e+01 bond pdb=" C ILE A 445 " pdb=" O ILE A 445 " ideal model delta sigma weight residual 1.237 1.176 0.062 1.32e-02 5.74e+03 2.19e+01 ... (remaining 24211 not shown) Histogram of bond angle deviations from ideal: 96.56 - 104.13: 415 104.13 - 111.70: 11010 111.70 - 119.27: 9897 119.27 - 126.84: 11194 126.84 - 134.41: 223 Bond angle restraints: 32739 Sorted by residual: angle pdb=" N GLN B 255 " pdb=" CA GLN B 255 " pdb=" C GLN B 255 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.17e+00 7.31e-01 6.14e+01 angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 111.62 105.50 6.12 7.90e-01 1.60e+00 5.99e+01 angle pdb=" N ILE B 370 " pdb=" CA ILE B 370 " pdb=" C ILE B 370 " ideal model delta sigma weight residual 111.90 105.67 6.23 8.10e-01 1.52e+00 5.91e+01 angle pdb=" N PHE A 563 " pdb=" CA PHE A 563 " pdb=" C PHE A 563 " ideal model delta sigma weight residual 113.41 104.19 9.22 1.22e+00 6.72e-01 5.71e+01 angle pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 120.83 125.26 -4.43 5.90e-01 2.87e+00 5.64e+01 ... (remaining 32734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 14170 35.13 - 70.27: 386 70.27 - 105.40: 28 105.40 - 140.54: 6 140.54 - 175.67: 7 Dihedral angle restraints: 14597 sinusoidal: 5839 harmonic: 8758 Sorted by residual: dihedral pdb=" C ASP B 153 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " ideal model delta harmonic sigma weight residual -122.60 -135.50 12.90 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" C GLU B 414 " pdb=" N GLU B 414 " pdb=" CA GLU B 414 " pdb=" CB GLU B 414 " ideal model delta harmonic sigma weight residual -122.60 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C THR B 489 " pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta harmonic sigma weight residual -122.00 -133.90 11.90 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 14594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3333 0.114 - 0.228: 419 0.228 - 0.342: 60 0.342 - 0.456: 10 0.456 - 0.571: 2 Chirality restraints: 3824 Sorted by residual: chirality pdb=" CB VAL A 905 " pdb=" CA VAL A 905 " pdb=" CG1 VAL A 905 " pdb=" CG2 VAL A 905 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" C6 PTY A1103 " pdb=" C1 PTY A1103 " pdb=" C5 PTY A1103 " pdb=" O7 PTY A1103 " both_signs ideal model delta sigma weight residual False 2.49 2.01 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" C6 PTY A1109 " pdb=" C1 PTY A1109 " pdb=" C5 PTY A1109 " pdb=" O7 PTY A1109 " both_signs ideal model delta sigma weight residual False 2.49 2.05 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 3821 not shown) Planarity restraints: 4127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 412 " -0.028 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C VAL C 412 " 0.097 2.00e-02 2.50e+03 pdb=" O VAL C 412 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL C 413 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 443 " 0.025 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C VAL A 443 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A 443 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY A 444 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 403 " 0.022 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C GLY A 403 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY A 403 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU A 404 " 0.027 2.00e-02 2.50e+03 ... (remaining 4124 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 420 2.66 - 3.22: 23338 3.22 - 3.78: 37345 3.78 - 4.34: 53727 4.34 - 4.90: 87600 Nonbonded interactions: 202430 Sorted by model distance: nonbonded pdb=" O ASN C 81 " pdb=" OD1 ASN C 81 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 345 " pdb=" CG2 ILE A 348 " model vdw 2.205 3.460 nonbonded pdb=" OG SER A 836 " pdb=" OE2 GLU A 839 " model vdw 2.212 2.440 nonbonded pdb=" OD1 ASP A 858 " pdb=" N TRP A 859 " model vdw 2.218 2.520 nonbonded pdb=" OD1 ASN A 415 " pdb=" OG SER A 434 " model vdw 2.242 2.440 ... (remaining 202425 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 163 or (resid 164 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 385 or (resid 386 an \ d (name N or name CA or name C or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 387 through 478 or (resid 479 and (n \ ame N or name CA or name C or name CB )) or resid 480 through 500 or resid 516 t \ hrough 1033 or (resid 1102 and (name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37)) or (resid 1103 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18)) or (resid 1104 and (na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 \ or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or (resid 1105 and (name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)))) selection = (chain 'B' and (resid 1 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 449 or (resid 450 and (name N or \ name CA or name C or name CB or name OG )) or resid 451 through 500 or resid 51 \ 6 through 517 or (resid 518 and (name N or name CA or name C or name O or name C \ B )) or resid 519 through 524 or (resid 525 and (name N or name CA or name C or \ name O or name CB )) or resid 526 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 or (resid 531 and (name N or n \ ame CA or name C or name O or name CB )) or resid 532 through 533 or (resid 534 \ and (name N or name CA or name C or name O or name CB )) or resid 535 or (resid \ 536 and (name N or name CA or name C or name O or name CB )) or resid 537 or (re \ sid 538 and (name N or name CA or name C or name O or name CB )) or resid 539 or \ (resid 540 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 1 through 619 or (resid 620 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name NE or name CZ )) or resid 621 through 846 or (re \ sid 847 through 848 and (name N or name CA or name C or name O or name CB )) or \ resid 849 through 954 or (resid 955 through 956 and (name N or name CA or name C \ or name O or name CB )) or resid 957 through 964 or (resid 965 and (name N or n \ ame CA or name C or name O or name CB )) or resid 966 through 968 or (resid 969 \ and (name N or name CA or name C or name O or name CB )) or resid 970 through 10 \ 25 or (resid 1026 through 1027 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1028 through 1030 or (resid 1031 through 1033 and (name N or na \ me CA or name C or name O or name CB )) or resid 1105 or (resid 1106 and (name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) or \ resid 1107 through 1108)) selection = (chain 'C' and (resid 1 through 163 or (resid 164 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 385 or (resid 386 an \ d (name N or name CA or name C or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 387 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 449 or ( \ resid 450 and (name N or name CA or name C or name CB or name OG )) or resid 451 \ through 478 or (resid 479 and (name N or name CA or name C or name CB )) or res \ id 480 through 500 or resid 516 through 521 or (resid 522 and (name N or name CA \ or name C or name O or name CB )) or resid 523 through 524 or (resid 525 and (n \ ame N or name CA or name C or name O or name CB )) or resid 526 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ or (resid 531 and (name N or name CA or name C or name O or name CB )) or resid \ 532 through 533 or (resid 534 and (name N or name CA or name C or name O or name \ CB )) or resid 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 or (resid 538 and (name N or name CA or name C or name O \ or name CB )) or resid 539 or (resid 540 and (name N or name CA or name C or na \ me O or name CB )) or resid 541 through 619 or (resid 620 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ )) o \ r resid 621 through 846 or (resid 847 through 848 and (name N or name CA or name \ C or name O or name CB )) or resid 849 through 954 or (resid 955 through 956 an \ d (name N or name CA or name C or name O or name CB )) or resid 957 through 964 \ or (resid 965 and (name N or name CA or name C or name O or name CB )) or resid \ 966 through 968 or (resid 969 and (name N or name CA or name C or name O or name \ CB )) or resid 970 through 1025 or (resid 1026 through 1027 and (name N or name \ CA or name C or name O or name CB )) or resid 1028 through 1030 or (resid 1031 \ through 1033 and (name N or name CA or name C or name O or name CB )) or (resid \ 1104 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37)) or (resid 1105 and (name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18)) or (resid 1106 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O1 \ 3 or name O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1107 and \ (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name N \ 1 )))) } 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: 2.440 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: 11.380 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 61.010 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.120 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.008 0.069 24216 Z= 0.543 Angle : 1.211 10.402 32739 Z= 0.858 Chirality : 0.078 0.571 3824 Planarity : 0.006 0.056 4127 Dihedral : 16.026 175.670 8977 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 2.99 % Favored : 96.56 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 2.22 % 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: -1.19 (0.15), residues: 3051 helix: -0.05 (0.13), residues: 1597 sheet: -1.68 (0.25), residues: 408 loop : -1.36 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 809 HIS 0.012 0.001 HIS A 526 PHE 0.031 0.002 PHE A 358 TYR 0.058 0.002 TYR A 49 ARG 0.007 0.000 ARG C 818 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 427 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 HIS cc_start: 0.8041 (t70) cc_final: 0.7840 (t-90) REVERT: B 407 ASP cc_start: 0.8236 (t70) cc_final: 0.7969 (t0) REVERT: B 573 MET cc_start: 0.7633 (mmt) cc_final: 0.7124 (mmt) REVERT: B 798 MET cc_start: 0.7342 (mtp) cc_final: 0.7133 (mmm) REVERT: A 174 ASP cc_start: 0.6700 (t70) cc_final: 0.5961 (t0) REVERT: A 904 VAL cc_start: 0.8603 (m) cc_final: 0.8150 (p) REVERT: A 1000 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7331 (tp-100) outliers start: 11 outliers final: 1 residues processed: 435 average time/residue: 0.3458 time to fit residues: 243.6258 Evaluate side-chains 289 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 683 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN B 231 ASN C 928 GLN A 577 GLN A 584 GLN A1000 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24216 Z= 0.204 Angle : 0.543 9.268 32739 Z= 0.282 Chirality : 0.042 0.170 3824 Planarity : 0.004 0.054 4127 Dihedral : 14.063 179.288 3720 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.21 % Allowed : 8.65 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.07 (0.16), residues: 3051 helix: 0.91 (0.13), residues: 1618 sheet: -1.49 (0.25), residues: 401 loop : -0.82 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 789 HIS 0.012 0.001 HIS A 526 PHE 0.022 0.001 PHE C 11 TYR 0.016 0.001 TYR B 877 ARG 0.005 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 338 HIS cc_start: 0.8075 (t70) cc_final: 0.7864 (t-90) REVERT: B 456 MET cc_start: 0.8344 (ttp) cc_final: 0.8102 (ttm) REVERT: B 525 HIS cc_start: 0.7724 (t70) cc_final: 0.7471 (t-90) REVERT: B 825 MET cc_start: 0.8155 (mtt) cc_final: 0.7800 (mtt) REVERT: C 184 MET cc_start: 0.8358 (tpp) cc_final: 0.7995 (tpt) REVERT: A 408 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8145 (m-30) outliers start: 30 outliers final: 19 residues processed: 331 average time/residue: 0.3202 time to fit residues: 176.8548 Evaluate side-chains 303 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 283 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 931 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 230 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 275 optimal weight: 0.0060 chunk 94 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 298 ASN C 74 ASN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24216 Z= 0.279 Angle : 0.534 9.381 32739 Z= 0.273 Chirality : 0.042 0.158 3824 Planarity : 0.004 0.048 4127 Dihedral : 12.825 175.383 3720 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.46 % Allowed : 10.88 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 3051 helix: 1.13 (0.13), residues: 1634 sheet: -1.36 (0.26), residues: 394 loop : -0.68 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 789 HIS 0.009 0.001 HIS A 526 PHE 0.019 0.001 PHE C 11 TYR 0.016 0.001 TYR C 541 ARG 0.007 0.000 ARG C 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 297 time to evaluate : 2.682 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 276 ASP cc_start: 0.7519 (m-30) cc_final: 0.7220 (m-30) REVERT: B 456 MET cc_start: 0.8408 (ttp) cc_final: 0.8198 (ttm) REVERT: B 525 HIS cc_start: 0.7802 (t70) cc_final: 0.7555 (t-90) REVERT: B 681 ASP cc_start: 0.7649 (t0) cc_final: 0.6817 (t0) REVERT: B 825 MET cc_start: 0.8275 (mtt) cc_final: 0.7947 (mtt) outliers start: 36 outliers final: 25 residues processed: 316 average time/residue: 0.3127 time to fit residues: 165.6122 Evaluate side-chains 300 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 275 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 937 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1001 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A1000 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24216 Z= 0.221 Angle : 0.501 8.714 32739 Z= 0.255 Chirality : 0.041 0.154 3824 Planarity : 0.004 0.049 4127 Dihedral : 12.085 172.221 3720 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.74 % Allowed : 11.73 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.45 (0.16), residues: 3051 helix: 1.31 (0.13), residues: 1627 sheet: -1.16 (0.25), residues: 413 loop : -0.59 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 PHE 0.018 0.001 PHE C 885 TYR 0.018 0.001 TYR C 541 ARG 0.004 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 301 time to evaluate : 2.591 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 276 ASP cc_start: 0.7527 (m-30) cc_final: 0.7231 (m-30) REVERT: B 525 HIS cc_start: 0.7777 (t70) cc_final: 0.7519 (t-90) REVERT: C 892 TYR cc_start: 0.8062 (m-10) cc_final: 0.7849 (m-80) REVERT: A 948 PHE cc_start: 0.7549 (m-10) cc_final: 0.7228 (m-80) outliers start: 43 outliers final: 25 residues processed: 326 average time/residue: 0.2983 time to fit residues: 163.5685 Evaluate side-chains 306 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 219 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1001 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24216 Z= 0.219 Angle : 0.500 8.027 32739 Z= 0.252 Chirality : 0.041 0.160 3824 Planarity : 0.003 0.048 4127 Dihedral : 11.675 178.399 3717 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.50 % Allowed : 12.82 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.57 (0.16), residues: 3051 helix: 1.41 (0.13), residues: 1620 sheet: -1.22 (0.25), residues: 405 loop : -0.49 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 789 HIS 0.008 0.001 HIS A 526 PHE 0.016 0.001 PHE C 885 TYR 0.017 0.001 TYR C 541 ARG 0.004 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 293 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 276 ASP cc_start: 0.7524 (m-30) cc_final: 0.7225 (m-30) REVERT: C 395 MET cc_start: 0.7924 (mmp) cc_final: 0.7695 (mmp) REVERT: C 892 TYR cc_start: 0.8054 (m-10) cc_final: 0.7853 (m-80) REVERT: A 948 PHE cc_start: 0.7569 (m-10) cc_final: 0.7248 (m-80) outliers start: 37 outliers final: 31 residues processed: 310 average time/residue: 0.3157 time to fit residues: 162.7750 Evaluate side-chains 316 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 285 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 5.9990 chunk 265 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 173 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A1000 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24216 Z= 0.154 Angle : 0.472 7.495 32739 Z= 0.239 Chirality : 0.040 0.146 3824 Planarity : 0.003 0.048 4127 Dihedral : 11.125 169.600 3717 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.78 % Allowed : 13.06 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.74 (0.16), residues: 3051 helix: 1.53 (0.13), residues: 1620 sheet: -1.07 (0.25), residues: 409 loop : -0.40 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 789 HIS 0.007 0.001 HIS A 526 PHE 0.020 0.001 PHE A 885 TYR 0.016 0.001 TYR C 541 ARG 0.002 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 276 ASP cc_start: 0.7524 (m-30) cc_final: 0.7219 (m-30) REVERT: A 29 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7506 (ttmt) REVERT: A 948 PHE cc_start: 0.7483 (m-10) cc_final: 0.7197 (m-80) outliers start: 44 outliers final: 27 residues processed: 329 average time/residue: 0.3065 time to fit residues: 167.2886 Evaluate side-chains 318 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 248 optimal weight: 0.0070 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 0.4980 chunk 183 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 89 GLN C 284 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24216 Z= 0.147 Angle : 0.465 7.710 32739 Z= 0.234 Chirality : 0.040 0.241 3824 Planarity : 0.003 0.048 4127 Dihedral : 10.692 158.373 3717 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 13.99 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.84 (0.16), residues: 3051 helix: 1.61 (0.13), residues: 1615 sheet: -0.99 (0.25), residues: 409 loop : -0.36 (0.21), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 789 HIS 0.006 0.000 HIS A 526 PHE 0.018 0.001 PHE A 352 TYR 0.024 0.001 TYR A 35 ARG 0.009 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 311 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 276 ASP cc_start: 0.7555 (m-30) cc_final: 0.7287 (m-30) REVERT: A 918 PHE cc_start: 0.6745 (m-80) cc_final: 0.6256 (t80) REVERT: A 948 PHE cc_start: 0.7404 (m-10) cc_final: 0.7076 (m-80) outliers start: 39 outliers final: 30 residues processed: 327 average time/residue: 0.3038 time to fit residues: 167.7792 Evaluate side-chains 321 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 291 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 924 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24216 Z= 0.154 Angle : 0.468 7.681 32739 Z= 0.235 Chirality : 0.040 0.210 3824 Planarity : 0.003 0.048 4127 Dihedral : 10.358 154.402 3717 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.66 % Allowed : 14.19 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.91 (0.16), residues: 3051 helix: 1.66 (0.13), residues: 1611 sheet: -0.92 (0.26), residues: 401 loop : -0.34 (0.21), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 789 HIS 0.006 0.000 HIS A 526 PHE 0.021 0.001 PHE A 885 TYR 0.014 0.001 TYR C 541 ARG 0.006 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 305 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: C 182 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: A 918 PHE cc_start: 0.6733 (m-80) cc_final: 0.6258 (t80) REVERT: A 948 PHE cc_start: 0.7396 (m-10) cc_final: 0.7084 (m-80) outliers start: 41 outliers final: 31 residues processed: 325 average time/residue: 0.3026 time to fit residues: 165.3712 Evaluate side-chains 327 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 295 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 247 optimal weight: 0.0170 chunk 259 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 830 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24216 Z= 0.160 Angle : 0.476 9.384 32739 Z= 0.238 Chirality : 0.040 0.205 3824 Planarity : 0.003 0.048 4127 Dihedral : 10.021 150.437 3717 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.58 % Allowed : 14.60 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.94 (0.16), residues: 3051 helix: 1.67 (0.13), residues: 1609 sheet: -0.89 (0.25), residues: 409 loop : -0.29 (0.21), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 789 HIS 0.006 0.000 HIS A 526 PHE 0.020 0.001 PHE A 352 TYR 0.014 0.001 TYR C 541 ARG 0.006 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 306 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 276 ASP cc_start: 0.7475 (m-30) cc_final: 0.7219 (m-30) REVERT: B 456 MET cc_start: 0.7841 (ttp) cc_final: 0.7625 (ttp) REVERT: C 182 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: A 918 PHE cc_start: 0.6738 (m-80) cc_final: 0.6303 (t80) REVERT: A 948 PHE cc_start: 0.7421 (m-10) cc_final: 0.7084 (m-80) outliers start: 39 outliers final: 37 residues processed: 328 average time/residue: 0.3089 time to fit residues: 170.2343 Evaluate side-chains 332 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 294 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 970 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 201 optimal weight: 0.3980 chunk 303 optimal weight: 0.0980 chunk 279 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24216 Z= 0.149 Angle : 0.475 8.970 32739 Z= 0.237 Chirality : 0.040 0.205 3824 Planarity : 0.003 0.048 4127 Dihedral : 9.716 146.164 3717 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.54 % Allowed : 14.96 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.96 (0.16), residues: 3051 helix: 1.68 (0.13), residues: 1611 sheet: -0.83 (0.25), residues: 411 loop : -0.29 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 789 HIS 0.006 0.000 HIS A 526 PHE 0.025 0.001 PHE A 885 TYR 0.032 0.001 TYR A 35 ARG 0.006 0.000 ARG A 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 310 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. REVERT: B 20 MET cc_start: 0.8365 (mtp) cc_final: 0.7888 (mtt) REVERT: B 456 MET cc_start: 0.7808 (ttp) cc_final: 0.7606 (ttp) REVERT: C 182 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: A 567 GLU cc_start: 0.7506 (pm20) cc_final: 0.7226 (pm20) REVERT: A 918 PHE cc_start: 0.6823 (m-80) cc_final: 0.6408 (t80) REVERT: A 948 PHE cc_start: 0.7357 (m-10) cc_final: 0.7016 (m-80) outliers start: 38 outliers final: 34 residues processed: 331 average time/residue: 0.3086 time to fit residues: 171.0922 Evaluate side-chains 337 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 781 MET Chi-restraints excluded: chain C residue 811 TYR Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** 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 = 0.3682 r_free = 0.3682 target = 0.128428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098140 restraints weight = 35858.562| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.39 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24216 Z= 0.202 Angle : 0.491 8.884 32739 Z= 0.246 Chirality : 0.041 0.204 3824 Planarity : 0.003 0.048 4127 Dihedral : 9.642 143.866 3717 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.62 % Allowed : 15.08 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.89 (0.16), residues: 3051 helix: 1.61 (0.13), residues: 1619 sheet: -0.90 (0.26), residues: 404 loop : -0.30 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 789 HIS 0.006 0.000 HIS A 526 PHE 0.023 0.001 PHE A 459 TYR 0.015 0.001 TYR A 35 ARG 0.008 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.11 seconds wall clock time: 93 minutes 49.99 seconds (5629.99 seconds total)