Starting phenix.real_space_refine on Thu Feb 15 06:24:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_31061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_31061.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_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_31061/02_2024/7ed5_31061_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_31061_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_31061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_31061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_31061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ed5_31061/02_2024/7ed5_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.42, per 1000 atoms: 0.56 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: 4.73 Conformation dependent library (CDL) restraints added in 2.2 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 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: 5.11 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: 4.12 Time building geometry restraints manager: 5.09 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: 6239 18.42 - 36.84: 572 36.84 - 55.25: 151 55.25 - 73.67: 69 73.67 - 92.09: 12 Dihedral angle restraints: 7043 sinusoidal: 3175 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 7040 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: 2.840 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: 7.390 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.190 Find NCS groups from input model: 0.350 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.070 ------------------------------------------------------------------------------- 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 : 16.357 92.088 4539 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 % Allowed : 2.18 % Favored : 94.24 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 268 HIS 0.006 0.001 HIS A 613 PHE 0.021 0.001 PHE B 147 TYR 0.013 0.001 TYR D 135 ARG 0.004 0.000 ARG D 96 *********************** 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 : 1.252 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8449 (mtp) cc_final: 0.8173 (mtp) REVERT: C 18 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8321 (tm-30) REVERT: D 166 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7929 (mm) outliers start: 41 outliers final: 13 residues processed: 176 average time/residue: 1.2978 time to fit residues: 247.9830 Evaluate side-chains 112 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 ILE 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: 0.1260 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= 0.260 Angle : 0.852 26.975 16129 Z= 0.367 Chirality : 0.094 2.215 1848 Planarity : 0.005 0.076 1890 Dihedral : 14.181 95.429 2125 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.11 % Favored : 92.43 % Rotamer: Outliers : 2.88 % Allowed : 9.95 % Favored : 87.17 % 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: -1.62 (0.23), residues: 1294 helix: -0.41 (0.21), residues: 601 sheet: -1.70 (0.39), residues: 157 loop : -1.51 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.015 0.001 PHE D 92 TYR 0.011 0.001 TYR A 867 ARG 0.006 0.000 ARG D 80 *********************** 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 134 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8455 (mtp) cc_final: 0.8183 (mtm) REVERT: B 70 MET cc_start: 0.8391 (tmm) cc_final: 0.7976 (pp-130) REVERT: D 166 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7803 (mm) REVERT: D 174 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5248 (mmt) REVERT: D 182 TRP cc_start: 0.6373 (OUTLIER) cc_final: 0.5238 (m100) outliers start: 33 outliers final: 17 residues processed: 123 average time/residue: 1.3560 time to fit residues: 180.3118 Evaluate side-chains 116 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP 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: 1.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.3282 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.1603 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= 0.229 Angle : 0.827 27.676 16129 Z= 0.349 Chirality : 0.093 2.143 1848 Planarity : 0.004 0.073 1890 Dihedral : 13.840 96.606 2109 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.57 % Favored : 92.19 % Rotamer: Outliers : 3.32 % Allowed : 11.52 % Favored : 85.17 % 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: -1.57 (0.23), residues: 1294 helix: -0.38 (0.21), residues: 608 sheet: -1.56 (0.39), residues: 155 loop : -1.53 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 PHE 0.014 0.001 PHE D 92 TYR 0.010 0.001 TYR A 788 ARG 0.006 0.000 ARG D 80 *********************** 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 141 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 1.241 Fit side-chains REVERT: A 466 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7831 (tp) REVERT: A 902 MET cc_start: 0.8442 (mtp) cc_final: 0.8175 (mtm) REVERT: B 70 MET cc_start: 0.8402 (tmm) cc_final: 0.8005 (pp-130) REVERT: C 62 MET cc_start: 0.6625 (pp-130) cc_final: 0.5934 (pp-130) REVERT: D 174 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5140 (mmt) REVERT: D 182 TRP cc_start: 0.6432 (OUTLIER) cc_final: 0.4892 (m100) outliers start: 38 outliers final: 17 residues processed: 132 average time/residue: 1.3519 time to fit residues: 193.0715 Evaluate side-chains 114 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP 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: 10.0000 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.8306 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11731 Z= 0.477 Angle : 0.908 27.760 16129 Z= 0.398 Chirality : 0.094 2.122 1848 Planarity : 0.005 0.080 1890 Dihedral : 13.939 96.071 2103 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.58 % Favored : 91.19 % Rotamer: Outliers : 4.10 % Allowed : 12.22 % Favored : 83.68 % 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: -1.93 (0.22), residues: 1294 helix: -0.64 (0.21), residues: 601 sheet: -1.97 (0.35), residues: 167 loop : -1.65 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.008 0.002 HIS C 36 PHE 0.025 0.002 PHE D 92 TYR 0.015 0.002 TYR A 80 ARG 0.006 0.001 ARG A 183 *********************** 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 146 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 99 time to evaluate : 1.334 Fit side-chains REVERT: A 668 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7667 (ttt) REVERT: A 902 MET cc_start: 0.8357 (mtp) cc_final: 0.8147 (mtm) REVERT: B 70 MET cc_start: 0.8378 (tmm) cc_final: 0.8009 (pp-130) REVERT: B 155 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: C 62 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.5779 (pp-130) REVERT: D 174 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.5137 (mmt) REVERT: D 182 TRP cc_start: 0.6698 (OUTLIER) cc_final: 0.5541 (m100) outliers start: 47 outliers final: 21 residues processed: 132 average time/residue: 1.3049 time to fit residues: 186.9933 Evaluate side-chains 121 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2026 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= 0.180 Angle : 0.822 27.611 16129 Z= 0.343 Chirality : 0.092 2.149 1848 Planarity : 0.004 0.073 1890 Dihedral : 13.660 94.666 2102 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.88 % Favored : 92.89 % Rotamer: Outliers : 2.62 % Allowed : 14.57 % Favored : 82.81 % 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: -1.65 (0.23), residues: 1294 helix: -0.44 (0.21), residues: 608 sheet: -1.68 (0.36), residues: 166 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.013 0.001 PHE A 652 TYR 0.012 0.001 TYR A 788 ARG 0.004 0.000 ARG A 183 *********************** 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 134 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.282 Fit side-chains REVERT: A 902 MET cc_start: 0.8502 (mtp) cc_final: 0.8248 (mtm) REVERT: B 67 MET cc_start: 0.8043 (tmm) cc_final: 0.7594 (ppp) REVERT: B 70 MET cc_start: 0.8377 (tmm) cc_final: 0.8019 (pp-130) REVERT: C 62 MET cc_start: 0.7053 (pp-130) cc_final: 0.5866 (pp-130) REVERT: D 174 MET cc_start: 0.5719 (OUTLIER) cc_final: 0.4974 (mmt) REVERT: D 182 TRP cc_start: 0.6430 (OUTLIER) cc_final: 0.4895 (m100) outliers start: 30 outliers final: 16 residues processed: 126 average time/residue: 1.3920 time to fit residues: 189.5568 Evaluate side-chains 118 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR 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: 0.5980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.8268 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11731 Z= 0.306 Angle : 0.852 27.608 16129 Z= 0.362 Chirality : 0.093 2.122 1848 Planarity : 0.004 0.077 1890 Dihedral : 13.649 93.923 2102 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.04 % Favored : 91.73 % Rotamer: Outliers : 3.58 % Allowed : 14.83 % Favored : 81.59 % 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: -1.66 (0.23), residues: 1294 helix: -0.43 (0.21), residues: 605 sheet: -1.75 (0.37), residues: 153 loop : -1.57 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.017 0.001 PHE D 92 TYR 0.012 0.001 TYR A 867 ARG 0.004 0.000 ARG A 183 *********************** 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 142 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 1.334 Fit side-chains REVERT: A 668 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7575 (ttt) REVERT: A 782 PHE cc_start: 0.8038 (t80) cc_final: 0.7526 (m-80) REVERT: A 902 MET cc_start: 0.8506 (mtp) cc_final: 0.8248 (mtm) REVERT: D 174 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.4984 (mmt) REVERT: D 182 TRP cc_start: 0.6579 (OUTLIER) cc_final: 0.5155 (m100) outliers start: 41 outliers final: 25 residues processed: 130 average time/residue: 1.3119 time to fit residues: 184.5157 Evaluate side-chains 126 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11731 Z= 0.235 Angle : 0.842 27.608 16129 Z= 0.355 Chirality : 0.092 2.121 1848 Planarity : 0.004 0.075 1890 Dihedral : 13.556 93.288 2102 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.58 % Rotamer: Outliers : 3.05 % Allowed : 15.53 % Favored : 81.41 % 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: -1.56 (0.23), residues: 1294 helix: -0.36 (0.21), residues: 603 sheet: -1.90 (0.37), residues: 143 loop : -1.43 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE D 92 TYR 0.011 0.001 TYR A 788 ARG 0.003 0.000 ARG A 183 *********************** 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 133 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.449 Fit side-chains REVERT: A 782 PHE cc_start: 0.8004 (t80) cc_final: 0.7502 (m-80) REVERT: A 902 MET cc_start: 0.8508 (mtp) cc_final: 0.8261 (mtm) REVERT: B 67 MET cc_start: 0.8129 (tmm) cc_final: 0.7508 (ppp) REVERT: B 70 MET cc_start: 0.8311 (tmm) cc_final: 0.8043 (pp-130) REVERT: C 62 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.5271 (pp-130) REVERT: D 174 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5072 (mmt) REVERT: D 182 TRP cc_start: 0.6506 (OUTLIER) cc_final: 0.4941 (m100) outliers start: 35 outliers final: 21 residues processed: 124 average time/residue: 1.3076 time to fit residues: 175.4853 Evaluate side-chains 121 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR 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: 2.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 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 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: 0.8303 moved from start: 0.2433 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= 0.431 Angle : 0.897 27.556 16129 Z= 0.389 Chirality : 0.093 2.108 1848 Planarity : 0.005 0.079 1890 Dihedral : 13.690 94.604 2101 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 3.32 % Allowed : 15.53 % Favored : 81.15 % 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: -1.78 (0.22), residues: 1294 helix: -0.57 (0.21), residues: 603 sheet: -2.06 (0.37), residues: 145 loop : -1.49 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.021 0.002 PHE D 92 TYR 0.022 0.002 TYR B 71 ARG 0.005 0.000 ARG A 183 *********************** 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 136 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 1.306 Fit side-chains REVERT: A 668 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7648 (ttt) REVERT: A 782 PHE cc_start: 0.8078 (t80) cc_final: 0.7556 (m-80) REVERT: A 902 MET cc_start: 0.8491 (mtp) cc_final: 0.8253 (mtm) REVERT: B 67 MET cc_start: 0.8207 (tmm) cc_final: 0.7571 (ppp) REVERT: B 155 GLU cc_start: 0.7598 (tt0) cc_final: 0.7360 (pp20) REVERT: C 62 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.5491 (pp-130) REVERT: D 69 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7741 (tm-30) REVERT: D 174 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5063 (mmt) REVERT: D 182 TRP cc_start: 0.6697 (OUTLIER) cc_final: 0.5686 (m100) outliers start: 38 outliers final: 20 residues processed: 127 average time/residue: 1.2560 time to fit residues: 174.4538 Evaluate side-chains 117 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 109 ASN D 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11731 Z= 0.192 Angle : 0.841 27.639 16129 Z= 0.354 Chirality : 0.092 2.136 1848 Planarity : 0.004 0.074 1890 Dihedral : 13.539 92.710 2101 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.03 % Favored : 92.74 % Rotamer: Outliers : 1.75 % Allowed : 17.63 % Favored : 80.63 % 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: -0.42 (0.21), residues: 602 sheet: -1.81 (0.37), residues: 155 loop : -1.41 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 652 TYR 0.019 0.001 TYR B 71 ARG 0.005 0.000 ARG D 111 *********************** 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 121 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.099 Fit side-chains REVERT: A 782 PHE cc_start: 0.7990 (t80) cc_final: 0.7428 (m-80) REVERT: A 902 MET cc_start: 0.8484 (mtp) cc_final: 0.8252 (mtm) REVERT: B 67 MET cc_start: 0.8174 (tmm) cc_final: 0.7374 (ppp) REVERT: C 62 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.5276 (pp-130) REVERT: D 174 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.4993 (mmt) REVERT: D 182 TRP cc_start: 0.6551 (OUTLIER) cc_final: 0.5095 (m100) outliers start: 20 outliers final: 15 residues processed: 116 average time/residue: 1.3668 time to fit residues: 171.5543 Evaluate side-chains 114 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- 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 69 GLN ** 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: 0.8238 moved from start: 0.2316 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= 0.219 Angle : 0.851 27.511 16129 Z= 0.359 Chirality : 0.092 2.119 1848 Planarity : 0.004 0.076 1890 Dihedral : 13.420 92.230 2101 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.04 % Rotamer: Outliers : 1.83 % Allowed : 17.54 % Favored : 80.63 % 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: -1.50 (0.23), residues: 1294 helix: -0.36 (0.21), residues: 603 sheet: -1.71 (0.37), residues: 155 loop : -1.36 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 162 HIS 0.007 0.001 HIS A 892 PHE 0.013 0.001 PHE A 652 TYR 0.019 0.001 TYR B 71 ARG 0.004 0.000 ARG D 111 ********************** 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 119 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.175 Fit side-chains REVERT: A 782 PHE cc_start: 0.8012 (t80) cc_final: 0.7452 (m-80) REVERT: A 847 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 902 MET cc_start: 0.8521 (mtp) cc_final: 0.8302 (mtm) REVERT: C 62 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.5320 (pp-130) REVERT: D 174 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5059 (mmt) outliers start: 21 outliers final: 16 residues processed: 114 average time/residue: 1.4117 time to fit residues: 173.7395 Evaluate side-chains 114 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 187 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.0020 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 108 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 69 GLN ** 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 = 0.3614 r_free = 0.3614 target = 0.097972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070880 restraints weight = 21066.861| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.34 r_work: 0.3025 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11731 Z= 0.248 Angle : 0.862 27.534 16129 Z= 0.366 Chirality : 0.092 2.121 1848 Planarity : 0.004 0.076 1890 Dihedral : 13.376 92.192 2101 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.57 % Favored : 92.19 % Rotamer: Outliers : 2.01 % Allowed : 17.45 % Favored : 80.54 % 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: -1.50 (0.23), residues: 1294 helix: -0.36 (0.21), residues: 603 sheet: -1.66 (0.37), residues: 153 loop : -1.40 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 182 HIS 0.007 0.001 HIS A 892 PHE 0.013 0.001 PHE A 652 TYR 0.018 0.001 TYR B 71 ARG 0.003 0.000 ARG A 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.76 seconds wall clock time: 72 minutes 17.86 seconds (4337.86 seconds total)