Starting phenix.real_space_refine (version: 1.19rc7) on Sun Dec 6 17:49:23 2020 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/12_2020/7ctt_30469_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6610 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 28, 'TRANS': 797} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 856 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "Q" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'RNA': 16} Modifications used: {'rna3p_pyr': 9, 'rna3p_pur': 7} Link IDs: {'rna3p': 15} Chain: "T" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 384 Classifications: {'RNA': 18} Modifications used: {'rna3p_pyr': 8, 'rna3p_pur': 10} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' ZN': 2, ' MG': 1, 'GE6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1801 SG CYS A 301 70.340 57.851 32.272 1.00 50.26 S ATOM 1842 SG CYS A 306 70.768 56.932 28.494 1.00 47.80 S ATOM 1874 SG CYS A 310 73.349 56.281 31.321 1.00 45.78 S ATOM 3267 SG CYS A 487 51.259 58.864 37.610 1.00 56.34 S ATOM 4520 SG CYS A 645 50.326 58.338 33.581 1.00 59.64 S ATOM 4526 SG CYS A 646 53.884 59.692 35.496 1.00 56.65 S Time building chain proxies: 5.53, per 1000 atoms: 0.62 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 8912 At special positions: 0 Unit cell: (112, 90, 104, 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 61 16.00 P 37 15.00 Mg 1 11.99 F 1 9.00 O 1770 8.00 N 1492 7.00 C 5548 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 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " 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 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 44.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.540A pdb=" N THR A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 169 through 198 removed outlier: 3.726A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.540A 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: 3.894A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.470A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 255' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.801A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.696A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.187A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.900A 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 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.658A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 639 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 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 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 853 through 871 removed outlier: 3.824A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.656A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 889 removed outlier: 4.241A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.896A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.999A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.908A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.846A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 101 through 110 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 334 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.815A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.721A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.451A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1387 1.32 - 1.44: 2751 1.44 - 1.56: 4870 1.56 - 1.69: 74 1.69 - 1.81: 94 Bond restraints: 9176 Sorted by residual: bond pdb=" C03 GE6 A1004 " pdb=" O01 GE6 A1004 " ideal model delta sigma weight residual 1.265 1.610 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C02 GE6 A1004 " pdb=" C03 GE6 A1004 " ideal model delta sigma weight residual 1.656 1.346 0.310 2.00e-02 2.50e+03 2.41e+02 bond pdb=" C10 GE6 A1004 " pdb=" O05 GE6 A1004 " ideal model delta sigma weight residual 1.185 1.490 -0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C01 GE6 A1004 " pdb=" C02 GE6 A1004 " ideal model delta sigma weight residual 1.240 1.491 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C04 GE6 A1004 " pdb=" O01 GE6 A1004 " ideal model delta sigma weight residual 1.524 1.284 0.240 2.00e-02 2.50e+03 1.44e+02 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.57: 293 105.57 - 112.67: 4895 112.67 - 119.78: 2983 119.78 - 126.88: 4293 126.88 - 133.98: 164 Bond angle restraints: 12628 Sorted by residual: angle pdb=" C VAL A 335 " pdb=" N ASP A 336 " pdb=" CA ASP A 336 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.54e+00 angle pdb=" C SER A 607 " pdb=" N ASP A 608 " pdb=" CA ASP A 608 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.25e+00 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.96e+00 angle pdb=" CA ARG A 553 " pdb=" C ARG A 553 " pdb=" O ARG A 553 " ideal model delta sigma weight residual 121.99 119.13 2.86 1.14e+00 7.69e-01 6.29e+00 angle pdb=" CA ASP A 623 " pdb=" C ASP A 623 " pdb=" O ASP A 623 " ideal model delta sigma weight residual 119.97 117.30 2.67 1.15e+00 7.56e-01 5.39e+00 ... (remaining 12623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4818 16.07 - 32.14: 407 32.14 - 48.21: 108 48.21 - 64.28: 14 64.28 - 80.35: 4 Dihedral angle restraints: 5351 sinusoidal: 2294 harmonic: 3057 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASP A 465 " pdb=" C ASP A 465 " pdb=" N ILE A 466 " pdb=" CA ILE A 466 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1191 0.049 - 0.097: 231 0.097 - 0.146: 35 0.146 - 0.194: 0 0.194 - 0.243: 1 Chirality restraints: 1458 Sorted by residual: chirality pdb=" C01 GE6 A1004 " pdb=" C02 GE6 A1004 " pdb=" C04 GE6 A1004 " pdb=" O03 GE6 A1004 " both_signs ideal model delta sigma weight residual False -2.36 -2.60 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASP A 336 " pdb=" N ASP A 336 " pdb=" C ASP A 336 " pdb=" CB ASP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ASP A 608 " pdb=" N ASP A 608 " pdb=" C ASP A 608 " pdb=" CB ASP A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1455 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C LEU A 758 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 191 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C GLN A 191 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN A 191 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 192 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 181 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C ARG A 181 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG A 181 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 182 " 0.010 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 230 2.68 - 3.23: 9062 3.23 - 3.79: 15033 3.79 - 4.34: 20608 4.34 - 4.90: 32390 Nonbonded interactions: 77323 Sorted by model distance: nonbonded pdb=" O ASN A 543 " pdb=" OG1 THR A 556 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR A 409 " pdb=" O GLN A 444 " model vdw 2.159 2.440 nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.164 2.440 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR A 226 " pdb=" OG SER A 229 " model vdw 2.237 2.440 ... (remaining 77318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 8912 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5548 2.51 5 N 1492 2.21 5 O 1770 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 0.620 Set model interpretation parameters: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.310 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.040 Process input model: 31.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.009 0.345 9176 Angle : 0.515 5.590 12628 Chirality : 0.039 0.243 1458 Planarity : 0.003 0.033 1481 Dihedral : 12.548 80.351 3375 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.22), residues: 1017 helix: -1.40 (0.20), residues: 456 sheet: -2.51 (0.52), residues: 63 loop : -2.17 (0.24), residues: 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.962 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 217 average time/residue: 0.2104 time to fit residues: 47.2503 Evaluate side-chains 177 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1138 time to fit residues: 1.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 492 GLN A 611 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 108 ASN C 18 GLN D 100 ASN D 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.046 9176 Angle : 0.609 7.666 12628 Chirality : 0.043 0.198 1458 Planarity : 0.004 0.085 1481 Dihedral : 6.331 47.928 1526 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.42 (0.24), residues: 1017 helix: -1.13 (0.21), residues: 485 sheet: -2.06 (0.55), residues: 63 loop : -1.98 (0.26), residues: 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.968 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 205 average time/residue: 0.2053 time to fit residues: 43.7780 Evaluate side-chains 176 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1377 time to fit residues: 1.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.039 9176 Angle : 0.534 5.866 12628 Chirality : 0.040 0.155 1458 Planarity : 0.004 0.082 1481 Dihedral : 6.065 47.418 1526 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 1017 helix: -0.52 (0.23), residues: 469 sheet: -1.93 (0.56), residues: 63 loop : -1.67 (0.27), residues: 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2187 time to fit residues: 47.8644 Evaluate side-chains 183 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.042 9176 Angle : 0.517 8.622 12628 Chirality : 0.039 0.235 1458 Planarity : 0.004 0.063 1481 Dihedral : 5.853 49.431 1526 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1017 helix: -0.14 (0.23), residues: 457 sheet: -1.69 (0.58), residues: 63 loop : -1.38 (0.27), residues: 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2102 time to fit residues: 47.6012 Evaluate side-chains 190 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 0.0570 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.045 9176 Angle : 0.489 6.807 12628 Chirality : 0.038 0.175 1458 Planarity : 0.003 0.055 1481 Dihedral : 5.720 53.624 1526 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1017 helix: 0.12 (0.24), residues: 455 sheet: -1.71 (0.62), residues: 63 loop : -1.05 (0.28), residues: 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2032 time to fit residues: 47.4021 Evaluate side-chains 181 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 99 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.041 9176 Angle : 0.516 6.238 12628 Chirality : 0.039 0.187 1458 Planarity : 0.003 0.051 1481 Dihedral : 5.734 54.178 1526 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1017 helix: 0.12 (0.24), residues: 466 sheet: -1.79 (0.52), residues: 85 loop : -0.99 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2052 time to fit residues: 45.9803 Evaluate side-chains 183 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 492 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.042 9176 Angle : 0.520 7.317 12628 Chirality : 0.040 0.193 1458 Planarity : 0.003 0.050 1481 Dihedral : 5.822 60.607 1526 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1017 helix: 0.08 (0.24), residues: 461 sheet: -1.57 (0.61), residues: 63 loop : -0.96 (0.28), residues: 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2038 time to fit residues: 45.9065 Evaluate side-chains 176 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.040 9176 Angle : 0.574 7.227 12628 Chirality : 0.041 0.202 1458 Planarity : 0.004 0.049 1481 Dihedral : 6.187 69.688 1526 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1017 helix: -0.13 (0.24), residues: 472 sheet: -1.73 (0.58), residues: 73 loop : -1.11 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.922 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2029 time to fit residues: 44.8392 Evaluate side-chains 180 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 0.0170 chunk 87 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 386 ASN A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.041 9176 Angle : 0.543 7.421 12628 Chirality : 0.040 0.332 1458 Planarity : 0.003 0.048 1481 Dihedral : 6.109 73.726 1526 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1017 helix: -0.04 (0.24), residues: 464 sheet: -1.51 (0.61), residues: 63 loop : -1.00 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2007 time to fit residues: 42.6726 Evaluate side-chains 171 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.051 9176 Angle : 0.534 7.833 12628 Chirality : 0.040 0.303 1458 Planarity : 0.003 0.047 1481 Dihedral : 6.060 72.898 1526 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1017 helix: -0.04 (0.24), residues: 470 sheet: -1.40 (0.62), residues: 63 loop : -0.87 (0.29), residues: 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield and 0 Emsley and 1017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2034 time to fit residues: 42.4222 Evaluate side-chains 174 residues out of total 910 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.0020 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.191067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154195 restraints weight = 10657.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158799 restraints weight = 5740.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.161666 restraints weight = 3923.568| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.043 9176 ANGLE : 0.519 7.829 12628 CHIRALITY : 0.039 0.280 1458 PLANARITY : 0.003 0.047 1481 DIHEDRAL : 6.058 79.446 1526 MIN NONBONDED DISTANCE : 2.170 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 11.15 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.23 % FAVORED : 95.77 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -0.83 (0.26), RESIDUES: 1017 HELIX: 0.03 (0.24), RESIDUES: 464 SHEET: -1.78 (0.52), RESIDUES: 85 LOOP : -0.79 (0.30), RESIDUES: 468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.043 9176 Angle : 0.519 7.829 12628 Chirality : 0.039 0.280 1458 Planarity : 0.003 0.047 1481 Dihedral : 6.058 79.446 1526 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1017 helix: 0.03 (0.24), residues: 464 sheet: -1.78 (0.52), residues: 85 loop : -0.79 (0.30), residues: 468 =============================================================================== Job complete usr+sys time: 1993.12 seconds wall clock time: 36 minutes 58.00 seconds (2218.00 seconds total)