Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 08:00:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/08_2023/7ed5_31061_updated.pdb" } resolution = 2.98 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= 0.001 sd= 0.028 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 50 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 7045 2.51 5 N 1925 2.21 5 O 2292 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 11402 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "B" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1169 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 144} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1201 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 3, ' ZN': 2, 'AT9': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'AT9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 17 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 54.176 94.058 52.298 1.00 64.51 S ATOM 2487 SG CYS A 306 52.297 97.020 50.292 1.00 66.43 S ATOM 2519 SG CYS A 310 52.305 93.094 49.123 1.00 61.12 S ATOM 3927 SG CYS A 487 55.120 94.893 72.914 1.00 67.35 S ATOM 5180 SG CYS A 645 53.900 98.359 71.717 1.00 71.35 S ATOM 5186 SG CYS A 646 56.127 96.145 69.478 1.00 71.14 S Time building chain proxies: 6.09, per 1000 atoms: 0.53 Number of scatterers: 11402 At special positions: 0 Unit cell: (90.47, 118.69, 146.08, 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 82 16.00 P 50 15.00 Mg 3 11.99 F 3 9.00 O 2292 8.00 N 1925 7.00 C 7045 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 1.6 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 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " 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 " Number of angles added : 6 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 9 sheets defined 41.8% alpha, 8.4% beta 13 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 176 through 199 removed outlier: 4.411A 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 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.016A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.256A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) 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 305 through 319 removed outlier: 3.572A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.160A 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 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.180A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.614A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (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 531 Processing helix chain 'A' and resid 562 through 572 removed outlier: 4.069A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.860A pdb=" N ILE A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 700 through 707 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.655A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 859 through 865 removed outlier: 3.512A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.903A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 918 through 924 removed outlier: 4.176A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 4.190A pdb=" N ASP B 50 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 93 removed outlier: 3.800A pdb=" N LEU B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 104 through 107 No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.882A 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 'C' and resid 3 through 6 No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.647A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 49 through 81 removed outlier: 3.505A pdb=" N ALA D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 3.510A pdb=" N ARG D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 135 through 140 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 71 through 74 removed outlier: 3.546A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 666 through 668 Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.843A pdb=" N TRP A 800 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 763 " --> pdb=" O MET A 756 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.539A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.880A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.094A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.195A 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 130 removed outlier: 5.695A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2391 1.33 - 1.46: 3521 1.46 - 1.59: 5598 1.59 - 1.71: 93 1.71 - 1.84: 128 Bond restraints: 11731 Sorted by residual: bond pdb=" C2' AT9 A1005 " pdb=" C3' AT9 A1005 " ideal model delta sigma weight residual 1.304 1.532 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C2' AT9 A1004 " pdb=" C3' AT9 A1004 " ideal model delta sigma weight residual 1.304 1.530 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C2' AT9 I 101 " pdb=" C3' AT9 I 101 " ideal model delta sigma weight residual 1.304 1.520 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" O3A AT9 I 101 " pdb=" PA AT9 I 101 " ideal model delta sigma weight residual 1.648 1.495 0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C4 AT9 I 101 " pdb=" N3 AT9 I 101 " ideal model delta sigma weight residual 1.493 1.350 0.143 2.00e-02 2.50e+03 5.09e+01 ... (remaining 11726 not shown) Histogram of bond angle deviations from ideal: 94.90 - 102.73: 172 102.73 - 110.56: 3514 110.56 - 118.39: 5588 118.39 - 126.22: 6594 126.22 - 134.05: 261 Bond angle restraints: 16129 Sorted by residual: angle pdb=" N ILE A 856 " pdb=" CA ILE A 856 " pdb=" C ILE A 856 " ideal model delta sigma weight residual 111.00 94.90 16.10 1.09e+00 8.42e-01 2.18e+02 angle pdb=" N ALA A 685 " pdb=" CA ALA A 685 " pdb=" C ALA A 685 " ideal model delta sigma weight residual 114.62 104.89 9.73 1.14e+00 7.69e-01 7.29e+01 angle pdb=" N SER A 904 " pdb=" CA SER A 904 " pdb=" C SER A 904 " ideal model delta sigma weight residual 113.88 103.38 10.50 1.23e+00 6.61e-01 7.28e+01 angle pdb=" N ALA D 181 " pdb=" CA ALA D 181 " pdb=" C ALA D 181 " ideal model delta sigma weight residual 109.76 97.20 12.56 1.59e+00 3.96e-01 6.24e+01 angle pdb=" N ASN A 911 " pdb=" CA ASN A 911 " pdb=" C ASN A 911 " ideal model delta sigma weight residual 111.71 101.24 10.47 1.34e+00 5.57e-01 6.10e+01 ... (remaining 16124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 6193 18.42 - 36.84: 549 36.84 - 55.25: 117 55.25 - 73.67: 25 73.67 - 92.09: 9 Dihedral angle restraints: 6893 sinusoidal: 3025 harmonic: 3868 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 147.81 32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" C THR D 145 " pdb=" N THR D 145 " pdb=" CA THR D 145 " pdb=" CB THR D 145 " ideal model delta harmonic sigma weight residual -122.00 -136.77 14.77 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" CA TYR A 149 " pdb=" C TYR A 149 " pdb=" N ASN A 150 " pdb=" CA ASN A 150 " ideal model delta harmonic sigma weight residual -180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 6890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.058: 1845 1.058 - 2.116: 0 2.116 - 3.174: 0 3.174 - 4.232: 0 4.232 - 5.290: 3 Chirality restraints: 1848 Sorted by residual: chirality pdb=" C2' AT9 I 101 " pdb=" C1' AT9 I 101 " pdb=" C3 AT9 I 101 " pdb=" C3' AT9 I 101 " both_signs ideal model delta sigma weight residual False 2.67 -2.62 5.29 2.00e-01 2.50e+01 6.99e+02 chirality pdb=" C2' AT9 A1005 " pdb=" C1' AT9 A1005 " pdb=" C3 AT9 A1005 " pdb=" C3' AT9 A1005 " both_signs ideal model delta sigma weight residual False 2.67 -2.57 5.24 2.00e-01 2.50e+01 6.87e+02 chirality pdb=" C2' AT9 A1004 " pdb=" C1' AT9 A1004 " pdb=" C3 AT9 A1004 " pdb=" C3' AT9 A1004 " both_signs ideal model delta sigma weight residual False 2.67 -2.57 5.24 2.00e-01 2.50e+01 6.85e+02 ... (remaining 1845 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 858 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 858 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 858 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE A 859 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 745 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE A 745 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE A 745 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR A 746 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 169 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C PRO A 169 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO A 169 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 170 " 0.018 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 219 2.66 - 3.22: 10518 3.22 - 3.78: 18731 3.78 - 4.34: 26723 4.34 - 4.90: 41759 Nonbonded interactions: 97950 Sorted by model distance: nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 2.094 2.170 nonbonded pdb=" OG1 THR A 246 " pdb=" O PRO A 461 " model vdw 2.162 2.440 nonbonded pdb=" OD1 ASP A 218 " pdb="MG MG A1007 " model vdw 2.214 2.170 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.243 2.440 nonbonded pdb=" OG SER A 501 " pdb=" OP1 C J 25 " model vdw 2.266 2.440 ... (remaining 97945 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 43 through 191) selection = (chain 'D' and ((resid 43 and (name N or name CA or name C or name O or name CB \ )) or resid 44 through 46 or (resid 47 and (name N or name CA or name C or name \ O or name CB )) or resid 48 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=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: 1.200 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: 0.010 Extract box with map and model: 7.570 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 36.160 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.009 0.228 11731 Z= 0.525 Angle : 0.904 16.096 16129 Z= 0.513 Chirality : 0.220 5.290 1848 Planarity : 0.004 0.073 1890 Dihedral : 14.585 92.088 4389 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 1.16 % Allowed : 6.72 % Favored : 92.12 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.51 (0.23), residues: 1294 helix: -0.35 (0.22), residues: 593 sheet: -1.40 (0.41), residues: 141 loop : -1.51 (0.26), residues: 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.203 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 13 residues processed: 176 average time/residue: 1.2008 time to fit residues: 229.7479 Evaluate side-chains 109 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.4690 time to fit residues: 3.3061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 892 HIS D 109 ASN D 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 11731 Z= 0.258 Angle : 0.855 26.871 16129 Z= 0.368 Chirality : 0.093 2.161 1848 Planarity : 0.005 0.076 1890 Dihedral : 8.040 95.780 1947 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.19 % Favored : 92.43 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1294 helix: -0.40 (0.21), residues: 601 sheet: -1.68 (0.39), residues: 157 loop : -1.51 (0.26), residues: 536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 1.309 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 129 average time/residue: 1.3507 time to fit residues: 188.2851 Evaluate side-chains 116 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.1385 time to fit residues: 1.7677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN D 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11731 Z= 0.201 Angle : 0.821 27.361 16129 Z= 0.345 Chirality : 0.093 2.135 1848 Planarity : 0.004 0.071 1890 Dihedral : 7.863 94.971 1947 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.34 % Favored : 92.43 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.52 (0.23), residues: 1294 helix: -0.35 (0.21), residues: 608 sheet: -1.48 (0.38), residues: 166 loop : -1.52 (0.27), residues: 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 1.265 Fit side-chains outliers start: 42 outliers final: 22 residues processed: 139 average time/residue: 1.3848 time to fit residues: 207.7124 Evaluate side-chains 119 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.1411 time to fit residues: 2.2687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 381 HIS A 524 GLN A 611 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 11731 Z= 0.434 Angle : 0.898 27.856 16129 Z= 0.390 Chirality : 0.093 2.108 1848 Planarity : 0.005 0.079 1890 Dihedral : 8.109 96.135 1947 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.27 % Favored : 91.50 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.84 (0.22), residues: 1294 helix: -0.61 (0.21), residues: 605 sheet: -1.78 (0.38), residues: 143 loop : -1.64 (0.26), residues: 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 1.438 Fit side-chains outliers start: 44 outliers final: 25 residues processed: 131 average time/residue: 1.3108 time to fit residues: 186.0182 Evaluate side-chains 122 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.1749 time to fit residues: 2.6434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 136 ASN D 109 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11731 Z= 0.224 Angle : 0.839 27.751 16129 Z= 0.354 Chirality : 0.092 2.124 1848 Planarity : 0.004 0.075 1890 Dihedral : 7.949 95.020 1947 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.11 % Favored : 92.66 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.69 (0.22), residues: 1294 helix: -0.47 (0.21), residues: 603 sheet: -1.82 (0.38), residues: 143 loop : -1.55 (0.25), residues: 548 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.303 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 131 average time/residue: 1.3347 time to fit residues: 188.9719 Evaluate side-chains 118 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 1.6464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN D 109 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 11731 Z= 0.435 Angle : 0.899 27.834 16129 Z= 0.391 Chirality : 0.093 2.106 1848 Planarity : 0.005 0.080 1890 Dihedral : 8.135 96.235 1947 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.35 % Favored : 91.42 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.91 (0.22), residues: 1294 helix: -0.65 (0.21), residues: 604 sheet: -1.92 (0.36), residues: 155 loop : -1.65 (0.26), residues: 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 1.262 Fit side-chains outliers start: 42 outliers final: 29 residues processed: 138 average time/residue: 1.3502 time to fit residues: 202.2290 Evaluate side-chains 126 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.5058 time to fit residues: 3.5555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN D 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11731 Z= 0.176 Angle : 0.834 27.863 16129 Z= 0.349 Chirality : 0.091 2.121 1848 Planarity : 0.004 0.073 1890 Dihedral : 7.866 94.059 1947 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.96 % Favored : 92.81 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.59 (0.23), residues: 1294 helix: -0.41 (0.21), residues: 601 sheet: -1.92 (0.37), residues: 143 loop : -1.42 (0.26), residues: 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.306 Fit side-chains outliers start: 36 outliers final: 25 residues processed: 135 average time/residue: 1.2847 time to fit residues: 188.4694 Evaluate side-chains 123 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 1.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 11731 Z= 0.486 Angle : 0.915 27.965 16129 Z= 0.400 Chirality : 0.094 2.099 1848 Planarity : 0.005 0.080 1890 Dihedral : 8.133 95.949 1947 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.91 (0.22), residues: 1294 helix: -0.68 (0.21), residues: 604 sheet: -1.93 (0.36), residues: 153 loop : -1.61 (0.26), residues: 537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 99 time to evaluate : 1.263 Fit side-chains outliers start: 41 outliers final: 28 residues processed: 131 average time/residue: 1.3556 time to fit residues: 192.0339 Evaluate side-chains 124 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.1121 time to fit residues: 2.5713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN D 43 ASN D 69 GLN D 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11731 Z= 0.191 Angle : 0.849 27.653 16129 Z= 0.359 Chirality : 0.091 2.127 1848 Planarity : 0.004 0.074 1890 Dihedral : 7.860 93.919 1947 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.42 % Favored : 92.35 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.23), residues: 1294 helix: -0.48 (0.21), residues: 603 sheet: -1.79 (0.37), residues: 155 loop : -1.42 (0.26), residues: 536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.431 Fit side-chains outliers start: 29 outliers final: 23 residues processed: 131 average time/residue: 1.3923 time to fit residues: 198.2189 Evaluate side-chains 119 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 1.7349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 892 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11731 Z= 0.181 Angle : 0.844 27.574 16129 Z= 0.354 Chirality : 0.091 2.102 1848 Planarity : 0.004 0.075 1890 Dihedral : 7.674 93.028 1947 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.58 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.44 (0.23), residues: 1294 helix: -0.32 (0.21), residues: 604 sheet: -1.69 (0.37), residues: 155 loop : -1.33 (0.26), residues: 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.281 Fit side-chains outliers start: 26 outliers final: 24 residues processed: 123 average time/residue: 1.3774 time to fit residues: 183.5469 Evaluate side-chains 119 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.5938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 892 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073220 restraints weight = 21618.932| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.30 r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 11731 Z= 0.243 Angle : 0.861 27.642 16129 Z= 0.364 Chirality : 0.091 2.105 1848 Planarity : 0.004 0.076 1890 Dihedral : 7.706 93.370 1947 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.42 % Favored : 92.35 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.48 (0.23), residues: 1294 helix: -0.37 (0.21), residues: 606 sheet: -1.65 (0.37), residues: 153 loop : -1.35 (0.26), residues: 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.24 seconds wall clock time: 70 minutes 30.55 seconds (4230.55 seconds total)