Starting phenix.real_space_refine on Wed Dec 13 15:20:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sq9_40699/12_2023/8sq9_40699_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.958 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 Mg 4 5.21 5 S 87 5.16 5 C 8027 2.51 5 N 2209 2.21 5 O 2923 1.98 5 H 12087 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25412 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 14726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 14659 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Conformer: "B" Number of residues, atoms: 926, 14659 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} bond proxies already assigned to first conformer: 14778 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2773 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1152 Classifications: {'peptide': 73} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2849 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1461 Classifications: {'peptide': 98} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Classifications: {'RNA': 32} Modifications used: {'3*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1122 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 33} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 250 Unusual residues: {' MG': 4, ' ZN': 2, 'WSB': 2} Classifications: {'undetermined': 8, 'water': 186} Link IDs: {None: 193} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "T" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4824 SG CYS A 301 31.115 87.929 108.501 1.00 78.43 S ATOM 4901 SG CYS A 306 32.066 91.480 109.803 1.00 82.22 S ATOM 4966 SG CYS A 310 32.955 88.054 111.554 1.00 68.52 S ATOM 7723 SG CYS A 487 29.931 89.626 87.986 1.00 61.74 S ATOM 10238 SG CYS A 645 30.043 92.848 88.727 1.00 69.49 S ATOM 10248 SG CYS A 646 28.660 90.357 91.035 1.00 79.21 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 41 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.50 residue: pdb=" N AARG A 726 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 726 " occ=0.50 Time building chain proxies: 16.79, per 1000 atoms: 0.66 Number of scatterers: 25412 At special positions: 0 Unit cell: (91.934, 135.763, 163.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 73 15.00 Mg 4 11.99 O 2923 8.00 N 2209 7.00 C 8027 6.00 H 12087 1.00 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: 22.25 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 11 sheets defined 45.9% alpha, 11.0% beta 26 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 13.96 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.525A pdb=" N HIS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.540A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 157 removed outlier: 3.781A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.746A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 236 through 247 Proline residue: A 243 - end of helix removed outlier: 3.843A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.671A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.548A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.912A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.528A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 4.222A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.961A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 removed outlier: 3.536A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 857 through 871 removed outlier: 3.570A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.660A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.709A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.619A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 removed outlier: 4.056A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 28 Processing helix chain 'B' and resid 32 through 97 removed outlier: 3.669A pdb=" N SER B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.511A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.534A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.558A pdb=" N VAL C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.724A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 174 through 179 Proline residue: D 178 - end of helix No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing helix chain 'G' and resid 96 through 104 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 102 through 106 removed outlier: 4.410A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE A 70 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS A 54 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.314A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= E, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.483A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.709A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 816 through 821 Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 5.832A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.152A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.685A pdb=" N ALA G 43 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN G 33 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL G 41 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 15 through 17 removed outlier: 4.283A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 10.08 Time building geometry restraints manager: 22.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12054 1.03 - 1.23: 344 1.23 - 1.43: 5640 1.43 - 1.63: 7399 1.63 - 1.82: 139 Bond restraints: 25576 Sorted by residual: bond pdb=" C2' WSB A1008 " pdb=" C3' WSB A1008 " ideal model delta sigma weight residual 1.262 1.522 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C2' WSB A1005 " pdb=" C3' WSB A1005 " ideal model delta sigma weight residual 1.262 1.520 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C1' WSB A1005 " pdb=" C2' WSB A1005 " ideal model delta sigma weight residual 1.676 1.524 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C1' WSB A1008 " pdb=" C2' WSB A1008 " ideal model delta sigma weight residual 1.676 1.525 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C LYS A 73 " pdb=" O LYS A 73 " ideal model delta sigma weight residual 1.234 1.149 0.085 1.22e-02 6.72e+03 4.86e+01 ... (remaining 25571 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.66: 675 106.66 - 113.51: 29293 113.51 - 120.36: 8886 120.36 - 127.21: 6925 127.21 - 134.06: 229 Bond angle restraints: 46008 Sorted by residual: angle pdb=" O LYS A 73 " pdb=" C LYS A 73 " pdb=" N ARG A 74 " ideal model delta sigma weight residual 123.27 118.26 5.01 1.16e+00 7.43e-01 1.86e+01 angle pdb=" CA ALYS A 73 " pdb=" C LYS A 73 " pdb=" N ARG A 74 " ideal model delta sigma weight residual 116.01 121.57 -5.56 1.51e+00 4.39e-01 1.36e+01 angle pdb=" PB WSB A1008 " pdb=" O3B WSB A1008 " pdb=" PG WSB A1008 " ideal model delta sigma weight residual 123.64 134.03 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C LYS A 574 " pdb=" N LEU A 575 " pdb=" CA LEU A 575 " ideal model delta sigma weight residual 120.28 116.01 4.27 1.34e+00 5.57e-01 1.01e+01 angle pdb=" C ASP A 618 " pdb=" N TYR A 619 " pdb=" CA TYR A 619 " ideal model delta sigma weight residual 120.49 116.50 3.99 1.42e+00 4.96e-01 7.88e+00 ... (remaining 46003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 11692 34.38 - 68.77: 239 68.77 - 103.15: 30 103.15 - 137.54: 6 137.54 - 171.92: 7 Dihedral angle restraints: 11974 sinusoidal: 6781 harmonic: 5193 Sorted by residual: dihedral pdb=" O4' G T 123 " pdb=" C1' G T 123 " pdb=" N9 G T 123 " pdb=" C4 G T 123 " ideal model delta sinusoidal sigma weight residual -106.00 -176.03 70.03 1 1.70e+01 3.46e-03 2.19e+01 dihedral pdb=" CA ASP A 465 " pdb=" C ASP A 465 " pdb=" N ILE A 466 " pdb=" CA ILE A 466 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN A 611 " pdb=" C ASN A 611 " pdb=" N PRO A 612 " pdb=" CA PRO A 612 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1905 0.055 - 0.111: 218 0.111 - 0.166: 34 0.166 - 0.221: 2 0.221 - 0.276: 4 Chirality restraints: 2163 Sorted by residual: chirality pdb=" C3' WSB A1005 " pdb=" C2' WSB A1005 " pdb=" C4' WSB A1005 " pdb=" O3' WSB A1005 " both_signs ideal model delta sigma weight residual False -2.39 -2.66 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' WSB A1008 " pdb=" C2' WSB A1008 " pdb=" C4' WSB A1008 " pdb=" O3' WSB A1008 " both_signs ideal model delta sigma weight residual False -2.39 -2.65 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ALYS A 73 " pdb=" N LYS A 73 " pdb=" C LYS A 73 " pdb=" CB ALYS A 73 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2160 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 73 " -0.080 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" O LYS A 73 " 0.030 2.00e-02 2.50e+03 pdb=" CA BLYS A 73 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 74 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 73 " -0.056 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" O LYS A 73 " 0.021 2.00e-02 2.50e+03 pdb=" CA ALYS A 73 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 74 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 72 " 0.013 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" N LYS A 73 " -0.042 2.00e-02 2.50e+03 pdb=" CA BLYS A 73 " 0.010 2.00e-02 2.50e+03 pdb=" H BLYS A 73 " 0.018 2.00e-02 2.50e+03 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1024 2.18 - 2.78: 48639 2.78 - 3.39: 69134 3.39 - 3.99: 93470 3.99 - 4.60: 144200 Nonbonded interactions: 356467 Sorted by model distance: nonbonded pdb="HH22 ARG A 733 " pdb=" O GLU G 3 " model vdw 1.575 1.850 nonbonded pdb=" H ASP D 161 " pdb=" O LYS D 165 " model vdw 1.588 1.850 nonbonded pdb=" O LYS D 39 " pdb="HD21 ASN D 43 " model vdw 1.599 1.850 nonbonded pdb=" O TYR A 915 " pdb=" HH TYR A 921 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP D 161 " pdb=" H ALA D 162 " model vdw 1.611 1.850 ... (remaining 356462 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 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 through 22 or (resid 23 t \ hrough 24 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 25 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 27 through 31 or (resid 3 \ 2 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 34 or (resid 35 through 37 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 38 through 39 or (resid 40 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 41 through 42 or (resid 43 and (name N or name CA or name C or name O or \ name CB or name HA )) or resid 44 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.150 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: 0.500 Extract box with map and model: 5.180 Check model and map are aligned: 0.390 Set scattering table: 0.270 Process input model: 107.780 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.007 0.260 13489 Z= 0.416 Angle : 0.551 10.391 18630 Z= 0.294 Chirality : 0.040 0.276 2163 Planarity : 0.003 0.046 2125 Dihedral : 14.556 116.562 5271 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.38 % Allowed : 6.50 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 (0.22), residues: 1462 helix: 1.28 (0.21), residues: 694 sheet: -0.74 (0.37), residues: 182 loop : -1.17 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.023 0.001 PHE A 571 TYR 0.013 0.001 TYR A 80 ARG 0.003 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 200 average time/residue: 2.0659 time to fit residues: 464.1031 Evaluate side-chains 164 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 1.2562 time to fit residues: 8.3374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS A 468 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13489 Z= 0.229 Angle : 0.484 5.463 18630 Z= 0.264 Chirality : 0.038 0.139 2163 Planarity : 0.004 0.042 2125 Dihedral : 13.635 117.322 2595 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 10.86 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.15 (0.22), residues: 1462 helix: 1.37 (0.21), residues: 691 sheet: -0.85 (0.36), residues: 188 loop : -1.09 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS A 725 PHE 0.014 0.001 PHE A 652 TYR 0.014 0.001 TYR A 80 ARG 0.006 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 167 average time/residue: 2.1218 time to fit residues: 396.5623 Evaluate side-chains 157 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.3531 time to fit residues: 3.8274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13489 Z= 0.410 Angle : 0.547 6.601 18630 Z= 0.300 Chirality : 0.041 0.163 2163 Planarity : 0.004 0.055 2125 Dihedral : 13.641 119.514 2595 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 2.78 % Allowed : 11.42 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.16 (0.22), residues: 1462 helix: 1.06 (0.20), residues: 701 sheet: -1.13 (0.36), residues: 181 loop : -1.17 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 290 HIS 0.008 0.002 HIS C 36 PHE 0.022 0.002 PHE A 571 TYR 0.018 0.002 TYR A 80 ARG 0.005 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 167 average time/residue: 2.0639 time to fit residues: 386.6753 Evaluate side-chains 157 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.3299 time to fit residues: 3.9247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 40.0000 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13489 Z= 0.211 Angle : 0.473 5.853 18630 Z= 0.257 Chirality : 0.037 0.152 2163 Planarity : 0.003 0.044 2125 Dihedral : 13.536 119.614 2595 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.46 % Allowed : 12.13 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.01 (0.22), residues: 1462 helix: 1.20 (0.21), residues: 707 sheet: -0.91 (0.35), residues: 186 loop : -1.16 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS A 725 PHE 0.017 0.001 PHE A 571 TYR 0.013 0.001 TYR A 80 ARG 0.004 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 166 average time/residue: 2.1893 time to fit residues: 406.2190 Evaluate side-chains 155 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.3915 time to fit residues: 3.4324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13489 Z= 0.311 Angle : 0.503 6.286 18630 Z= 0.274 Chirality : 0.039 0.165 2163 Planarity : 0.004 0.046 2125 Dihedral : 13.529 120.957 2595 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 2.22 % Allowed : 12.77 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.04 (0.22), residues: 1462 helix: 1.16 (0.20), residues: 707 sheet: -0.99 (0.36), residues: 181 loop : -1.16 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.016 0.002 PHE A 741 TYR 0.022 0.001 TYR A 32 ARG 0.004 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 163 average time/residue: 2.0466 time to fit residues: 375.8560 Evaluate side-chains 159 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.3472 time to fit residues: 3.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13489 Z= 0.280 Angle : 0.494 6.373 18630 Z= 0.267 Chirality : 0.038 0.162 2163 Planarity : 0.003 0.046 2125 Dihedral : 13.511 121.404 2595 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.85 % Allowed : 12.61 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.02 (0.22), residues: 1462 helix: 1.22 (0.21), residues: 706 sheet: -0.95 (0.36), residues: 181 loop : -1.14 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 80 ARG 0.007 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 27 residues processed: 160 average time/residue: 2.0674 time to fit residues: 375.0049 Evaluate side-chains 162 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.4027 time to fit residues: 5.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 40.0000 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13489 Z= 0.176 Angle : 0.459 5.985 18630 Z= 0.246 Chirality : 0.036 0.153 2163 Planarity : 0.003 0.043 2125 Dihedral : 13.462 121.780 2595 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.46 % Allowed : 12.93 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.27 (0.23), residues: 1462 helix: 1.43 (0.21), residues: 699 sheet: -0.84 (0.36), residues: 181 loop : -1.00 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS A 572 PHE 0.013 0.001 PHE A 571 TYR 0.012 0.001 TYR A 80 ARG 0.007 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 164 average time/residue: 2.0868 time to fit residues: 390.8089 Evaluate side-chains 158 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.3583 time to fit residues: 3.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13489 Z= 0.301 Angle : 0.498 6.645 18630 Z= 0.270 Chirality : 0.039 0.162 2163 Planarity : 0.003 0.045 2125 Dihedral : 13.496 122.816 2595 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 2.30 % Allowed : 13.56 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.14 (0.22), residues: 1462 helix: 1.32 (0.21), residues: 707 sheet: -0.90 (0.36), residues: 181 loop : -1.09 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 572 PHE 0.015 0.002 PHE A 741 TYR 0.015 0.001 TYR A 80 ARG 0.008 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 160 average time/residue: 2.0167 time to fit residues: 364.7294 Evaluate side-chains 159 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.6320 time to fit residues: 4.1048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13489 Z= 0.345 Angle : 0.518 5.786 18630 Z= 0.282 Chirality : 0.040 0.161 2163 Planarity : 0.004 0.050 2125 Dihedral : 13.568 123.462 2595 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.38 % Allowed : 13.56 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.04 (0.22), residues: 1462 helix: 1.28 (0.21), residues: 697 sheet: -1.01 (0.36), residues: 181 loop : -1.14 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.002 PHE A 741 TYR 0.017 0.002 TYR A 80 ARG 0.009 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 24 residues processed: 160 average time/residue: 2.0759 time to fit residues: 375.8513 Evaluate side-chains 157 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.4906 time to fit residues: 4.6044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 0.0060 chunk 149 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13489 Z= 0.182 Angle : 0.466 5.505 18630 Z= 0.251 Chirality : 0.037 0.150 2163 Planarity : 0.003 0.049 2125 Dihedral : 13.522 123.261 2595 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 1.74 % Allowed : 14.04 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.32 (0.23), residues: 1462 helix: 1.52 (0.21), residues: 696 sheet: -0.93 (0.36), residues: 181 loop : -0.98 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 572 PHE 0.013 0.001 PHE A 652 TYR 0.013 0.001 TYR A 80 ARG 0.009 0.000 ARG A 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 21 residues processed: 155 average time/residue: 2.0185 time to fit residues: 353.0021 Evaluate side-chains 154 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 2.3553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** 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 = 0.3969 r_free = 0.3969 target = 0.175794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122341 restraints weight = 53217.327| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.02 r_work: 0.2977 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13489 Z= 0.151 Angle : 0.451 6.769 18630 Z= 0.241 Chirality : 0.036 0.142 2163 Planarity : 0.003 0.045 2125 Dihedral : 13.463 123.730 2595 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 1.82 % Allowed : 14.04 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 (0.23), residues: 1462 helix: 1.60 (0.21), residues: 700 sheet: -0.91 (0.36), residues: 181 loop : -0.88 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 572 PHE 0.011 0.001 PHE D 92 TYR 0.012 0.001 TYR G 32 ARG 0.008 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8459.54 seconds wall clock time: 149 minutes 48.21 seconds (8988.21 seconds total)