Starting phenix.real_space_refine (version: dev) on Sun Feb 19 15:22:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gna_34158/02_2023/8gna_34158.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gna_34158/02_2023/8gna_34158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gna_34158/02_2023/8gna_34158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gna_34158/02_2023/8gna_34158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gna_34158/02_2023/8gna_34158.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gna_34158/02_2023/8gna_34158.pdb" } resolution = 2.8 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= 1.000 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 Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10257 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9213 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 59, 'TRANS': 1128} Chain breaks: 16 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 12, 'ASP:plan': 23, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 285 Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 666 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 1, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 13} Chain: "J" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3206 SG CYS A 491 47.308 52.523 101.159 1.00 43.52 S ATOM 3274 SG CYS A 501 47.555 52.621 104.833 1.00 47.64 S ATOM 3288 SG CYS A 503 44.681 54.365 103.302 1.00 45.64 S ATOM 3310 SG CYS A 506 44.605 50.647 103.129 1.00 40.94 S ATOM 644 SG CYS A 88 39.765 40.427 132.198 1.00 65.88 S ATOM 852 SG CYS A 121 40.171 38.526 135.417 1.00 79.39 S ATOM 883 SG CYS A 127 36.773 38.593 133.814 1.00 67.21 S ATOM 907 SG CYS A 130 39.760 36.779 132.037 1.00 64.85 S ATOM 5172 SG CYS A 750 56.150 57.879 73.817 1.00 56.51 S ATOM 5185 SG CYS A 752 53.020 59.011 72.136 1.00 48.44 S ATOM 5207 SG CYS A 755 52.874 55.748 73.926 1.00 45.65 S ATOM 7073 SG CYS A1018 51.365 43.491 39.396 1.00 41.19 S ATOM 7231 SG CYS A1406 53.584 44.149 42.474 1.00 48.81 S ATOM 7282 SG CYS A1414 53.454 46.347 39.428 1.00 40.01 S ATOM 7299 SG CYS A1417 50.257 45.905 41.964 1.00 35.80 S Time building chain proxies: 6.85, per 1000 atoms: 0.67 Number of scatterers: 10257 At special positions: 0 Unit cell: (71.25, 84.55, 148.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 31 16.00 P 49 15.00 O 1980 8.00 N 1799 7.00 C 6394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 21 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 30.9% alpha, 22.1% beta 12 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.569A pdb=" N MET A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.544A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.540A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.641A pdb=" N ILE A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 623 " --> pdb=" O ASN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.713A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 removed outlier: 3.652A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.570A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.606A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 removed outlier: 3.551A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 910 through 914 removed outlier: 4.141A pdb=" N ASP A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 Processing helix chain 'A' and resid 1395 through 1399 removed outlier: 3.750A pdb=" N LEU A1399 " --> pdb=" O GLY A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.100A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.713A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.794A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1588 Processing helix chain 'A' and resid 1590 through 1601 Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1630 Processing helix chain 'A' and resid 1675 through 1681 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.754A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.754A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 238 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.914A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 180 through 181 removed outlier: 7.131A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 4.548A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.463A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 533 removed outlier: 6.429A pdb=" N SER A 544 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 721 through 722 removed outlier: 4.135A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 722 removed outlier: 4.135A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.956A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB7, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.733A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.733A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.327A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.555A pdb=" N GLU A 995 " --> pdb=" O ILE A 992 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1453 through 1455 Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1648 removed outlier: 6.492A pdb=" N VAL A1647 " --> pdb=" O TYR A1663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 353 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2967 1.34 - 1.45: 2028 1.45 - 1.57: 5460 1.57 - 1.69: 96 1.69 - 1.81: 42 Bond restraints: 10593 Sorted by residual: bond pdb=" O5' C C -16 " pdb=" C5' C C -16 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.13e+00 bond pdb=" O5' A C -17 " pdb=" C5' A C -17 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.87e+00 bond pdb=" P A C -17 " pdb=" OP1 A C -17 " ideal model delta sigma weight residual 1.485 1.516 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" P A C -17 " pdb=" OP2 A C -17 " ideal model delta sigma weight residual 1.485 1.515 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" O5' U C -14 " pdb=" C5' U C -14 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 1.98e+00 ... (remaining 10588 not shown) Histogram of bond angle deviations from ideal: 94.07 - 102.07: 60 102.07 - 110.08: 2190 110.08 - 118.08: 6036 118.08 - 126.09: 5939 126.09 - 134.09: 330 Bond angle restraints: 14555 Sorted by residual: angle pdb=" C3' C C -16 " pdb=" O3' C C -16 " pdb=" P U C -15 " ideal model delta sigma weight residual 120.20 103.70 16.50 1.50e+00 4.44e-01 1.21e+02 angle pdb=" C4' U C -15 " pdb=" C3' U C -15 " pdb=" C2' U C -15 " ideal model delta sigma weight residual 102.60 94.07 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" C3' A C -17 " pdb=" O3' A C -17 " pdb=" P C C -16 " ideal model delta sigma weight residual 120.20 110.10 10.10 1.50e+00 4.44e-01 4.54e+01 angle pdb=" C3' U C -14 " pdb=" O3' U C -14 " pdb=" P A C -13 " ideal model delta sigma weight residual 120.20 112.54 7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" O4' U C -15 " pdb=" C4' U C -15 " pdb=" C3' U C -15 " ideal model delta sigma weight residual 104.00 99.85 4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 14550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 6010 35.29 - 70.58: 140 70.58 - 105.87: 8 105.87 - 141.17: 2 141.17 - 176.46: 2 Dihedral angle restraints: 6162 sinusoidal: 2778 harmonic: 3384 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual -128.00 48.46 -176.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 39.56 -167.56 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" CA GLU A1589 " pdb=" C GLU A1589 " pdb=" N TYR A1590 " pdb=" CA TYR A1590 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 6159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1601 0.116 - 0.232: 23 0.232 - 0.347: 4 0.347 - 0.463: 0 0.463 - 0.579: 1 Chirality restraints: 1629 Sorted by residual: chirality pdb=" P A C -17 " pdb=" OP1 A C -17 " pdb=" OP2 A C -17 " pdb=" O5' A C -17 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" P U C -14 " pdb=" OP1 U C -14 " pdb=" OP2 U C -14 " pdb=" O5' U C -14 " both_signs ideal model delta sigma weight residual True 2.41 -2.74 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" P C C -16 " pdb=" OP1 C C -16 " pdb=" OP2 C C -16 " pdb=" O5' C C -16 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1626 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U C -15 " 0.034 2.00e-02 2.50e+03 1.88e-02 7.94e+00 pdb=" N1 U C -15 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U C -15 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U C -15 " -0.015 2.00e-02 2.50e+03 pdb=" N3 U C -15 " 0.019 2.00e-02 2.50e+03 pdb=" C4 U C -15 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U C -15 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U C -15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U C -15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 11 " -0.030 2.00e-02 2.50e+03 1.45e-02 6.34e+00 pdb=" N9 G C 11 " 0.039 2.00e-02 2.50e+03 pdb=" C8 G C 11 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G C 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G C 11 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G C 11 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G C 11 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G C 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 11 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 11 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C -2 " -0.030 2.00e-02 2.50e+03 1.37e-02 5.19e+00 pdb=" N9 A C -2 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A C -2 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A C -2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C -2 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C -2 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A C -2 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A C -2 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A C -2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C -2 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C -2 " 0.006 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 328 2.68 - 3.23: 9850 3.23 - 3.79: 17440 3.79 - 4.34: 24763 4.34 - 4.90: 39241 Nonbonded interactions: 91622 Sorted by model distance: nonbonded pdb=" OH TYR A 922 " pdb=" OP2 C C 15 " model vdw 2.125 2.440 nonbonded pdb=" O GLY A 186 " pdb=" O2' C C -1 " model vdw 2.173 2.440 nonbonded pdb=" O ASP A 801 " pdb=" O2' C J 28 " model vdw 2.195 2.440 nonbonded pdb=" OE1 GLU A 465 " pdb=" NH2 ARG A 467 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR A 934 " pdb=" OE1 GLU A 936 " model vdw 2.205 2.440 ... (remaining 91617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 49 5.49 5 S 31 5.16 5 C 6394 2.51 5 N 1799 2.21 5 O 1980 1.98 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 Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 6.680 Check model and map are aligned: 0.140 Process input model: 38.410 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 59.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.003 0.033 10593 Z= 0.168 Angle : 0.576 16.496 14555 Z= 0.319 Chirality : 0.045 0.579 1629 Planarity : 0.004 0.050 1676 Dihedral : 15.035 176.458 3988 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % 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: -0.88 (0.24), residues: 1154 helix: 0.25 (0.31), residues: 289 sheet: -0.69 (0.43), residues: 141 loop : -0.91 (0.23), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.321 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 1.2390 time to fit residues: 209.1001 Evaluate side-chains 104 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.0020 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10593 Z= 0.211 Angle : 0.571 7.377 14555 Z= 0.298 Chirality : 0.043 0.343 1629 Planarity : 0.004 0.047 1676 Dihedral : 12.969 176.780 1857 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.94 % 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: -0.78 (0.25), residues: 1154 helix: 0.51 (0.30), residues: 310 sheet: -0.59 (0.40), residues: 165 loop : -0.99 (0.24), residues: 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.142 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 1.1052 time to fit residues: 153.6434 Evaluate side-chains 104 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.9713 time to fit residues: 3.7210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 110 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 287 ASN A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10593 Z= 0.175 Angle : 0.528 7.399 14555 Z= 0.278 Chirality : 0.042 0.355 1629 Planarity : 0.004 0.047 1676 Dihedral : 13.002 176.270 1857 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 2.16 % 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: -0.65 (0.25), residues: 1154 helix: 0.69 (0.30), residues: 313 sheet: -0.60 (0.39), residues: 166 loop : -0.93 (0.24), residues: 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.057 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 1.0640 time to fit residues: 141.6181 Evaluate side-chains 103 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.7125 time to fit residues: 4.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS A 287 ASN A 502 ASN A 696 ASN A 980 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 10593 Z= 0.315 Angle : 0.604 8.920 14555 Z= 0.312 Chirality : 0.045 0.373 1629 Planarity : 0.005 0.050 1676 Dihedral : 13.135 177.682 1857 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 3.56 % 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: -0.88 (0.24), residues: 1154 helix: 0.44 (0.29), residues: 319 sheet: -0.60 (0.37), residues: 176 loop : -1.09 (0.24), residues: 659 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.041 Fit side-chains outliers start: 33 outliers final: 12 residues processed: 128 average time/residue: 1.1480 time to fit residues: 160.6753 Evaluate side-chains 100 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1079 time to fit residues: 2.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 10593 Z= 0.293 Angle : 0.588 7.707 14555 Z= 0.307 Chirality : 0.045 0.374 1629 Planarity : 0.004 0.049 1676 Dihedral : 13.151 176.938 1857 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 3.67 % 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 (0.24), residues: 1154 helix: 0.41 (0.29), residues: 319 sheet: -0.70 (0.36), residues: 176 loop : -1.12 (0.24), residues: 659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 1.265 Fit side-chains outliers start: 34 outliers final: 19 residues processed: 128 average time/residue: 1.0637 time to fit residues: 149.7630 Evaluate side-chains 107 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 0.1232 time to fit residues: 2.2252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10593 Z= 0.214 Angle : 0.548 7.639 14555 Z= 0.287 Chirality : 0.043 0.370 1629 Planarity : 0.004 0.048 1676 Dihedral : 13.093 176.384 1857 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 3.78 % 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: -0.78 (0.24), residues: 1154 helix: 0.65 (0.30), residues: 316 sheet: -0.71 (0.36), residues: 176 loop : -1.04 (0.24), residues: 662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 1.181 Fit side-chains outliers start: 35 outliers final: 19 residues processed: 127 average time/residue: 1.0282 time to fit residues: 144.2669 Evaluate side-chains 107 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.1245 time to fit residues: 2.7727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.0570 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10593 Z= 0.177 Angle : 0.532 7.590 14555 Z= 0.279 Chirality : 0.042 0.369 1629 Planarity : 0.004 0.046 1676 Dihedral : 13.010 176.133 1857 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 2.92 % 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: -0.65 (0.24), residues: 1154 helix: 0.80 (0.30), residues: 316 sheet: -0.69 (0.37), residues: 166 loop : -0.97 (0.24), residues: 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.135 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 129 average time/residue: 1.0376 time to fit residues: 147.8727 Evaluate side-chains 111 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1277 time to fit residues: 2.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10593 Z= 0.223 Angle : 0.550 7.683 14555 Z= 0.286 Chirality : 0.043 0.374 1629 Planarity : 0.004 0.048 1676 Dihedral : 13.017 176.765 1857 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 2.81 % 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: -0.68 (0.24), residues: 1154 helix: 0.78 (0.30), residues: 316 sheet: -0.64 (0.36), residues: 172 loop : -1.01 (0.24), residues: 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.164 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 1.0333 time to fit residues: 133.9003 Evaluate side-chains 109 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1358 time to fit residues: 2.5778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 86 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10593 Z= 0.153 Angle : 0.524 7.920 14555 Z= 0.274 Chirality : 0.042 0.375 1629 Planarity : 0.004 0.045 1676 Dihedral : 12.952 175.747 1857 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 2.48 % 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: -0.55 (0.25), residues: 1154 helix: 0.99 (0.30), residues: 315 sheet: -0.74 (0.36), residues: 167 loop : -0.93 (0.24), residues: 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.223 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 0.9623 time to fit residues: 136.4170 Evaluate side-chains 116 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1676 time to fit residues: 2.5566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.0570 chunk 10 optimal weight: 0.0050 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 348 GLN A 502 ASN A 696 ASN A 980 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10593 Z= 0.173 Angle : 0.540 11.808 14555 Z= 0.277 Chirality : 0.043 0.370 1629 Planarity : 0.004 0.045 1676 Dihedral : 12.913 176.359 1857 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 2.48 % 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: -0.52 (0.25), residues: 1154 helix: 0.98 (0.30), residues: 315 sheet: -0.75 (0.35), residues: 186 loop : -0.87 (0.25), residues: 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.176 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 123 average time/residue: 0.9795 time to fit residues: 133.7463 Evaluate side-chains 112 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1387 time to fit residues: 2.1720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 502 ASN A 696 ASN A 980 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140124 restraints weight = 11047.725| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.62 r_work: 0.3602 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10593 Z= 0.289 Angle : 0.601 10.950 14555 Z= 0.307 Chirality : 0.045 0.377 1629 Planarity : 0.004 0.048 1676 Dihedral : 13.027 177.374 1857 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 2.38 % 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: -0.66 (0.25), residues: 1154 helix: 0.79 (0.30), residues: 315 sheet: -0.73 (0.35), residues: 191 loop : -0.94 (0.25), residues: 648 =============================================================================== Job complete usr+sys time: 3334.34 seconds wall clock time: 61 minutes 2.47 seconds (3662.47 seconds total)