Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 13:06:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/10_2023/7c2k_30275_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/10_2023/7c2k_30275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/10_2023/7c2k_30275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/10_2023/7c2k_30275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/10_2023/7c2k_30275_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/10_2023/7c2k_30275_updated.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 32 5.49 5 S 77 5.16 5 C 6667 2.51 5 N 1806 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ASP 29": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10692 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7464 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 554 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "G" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'F86': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8, None: 2} Not linked: pdbres=" G G 3 " pdbres="F86 G 4 " Not linked: pdbres="F86 G 4 " pdbres=" G G 5 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2538 SG CYS A 310 75.724 40.795 50.289 1.00 27.08 S ATOM 3946 SG CYS A 487 88.847 46.521 69.558 1.00 31.06 S ATOM 5199 SG CYS A 645 90.765 48.370 66.495 1.00 36.06 S ATOM 5205 SG CYS A 646 88.957 44.100 65.770 1.00 34.53 S Time building chain proxies: 6.22, per 1000 atoms: 0.58 Number of scatterers: 10692 At special positions: 0 Unit cell: (104.14, 100.86, 132.84, 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 2 29.99 S 77 16.00 P 32 15.00 O 2108 8.00 N 1806 7.00 C 6667 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 11 sheets defined 44.7% alpha, 9.7% beta 14 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.719A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.514A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.065A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.460A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 4.523A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.078A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 4.049A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.924A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.728A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 removed outlier: 3.512A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 856 through 871 Proline residue: A 868 - end of helix removed outlier: 4.640A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.841A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.816A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.867A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.901A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 54 through 82 removed outlier: 3.658A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.771A pdb=" N ASN D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.039A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 33 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 70 through 73 Processing sheet with id= D, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.734A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 330 through 334 Processing sheet with id= F, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= G, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.565A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= I, first strand: chain 'A' and resid 816 through 821 Processing sheet with id= J, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.704A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 128 through 132 402 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1689 1.27 - 1.40: 2878 1.40 - 1.54: 6175 1.54 - 1.67: 125 1.67 - 1.81: 118 Bond restraints: 10985 Sorted by residual: bond pdb=" C1 F86 G 4 " pdb=" C5 F86 G 4 " ideal model delta sigma weight residual 1.507 1.381 0.126 1.00e-02 1.00e+04 1.59e+02 bond pdb=" C4 F86 G 4 " pdb=" O1 F86 G 4 " ideal model delta sigma weight residual 1.435 1.284 0.151 1.20e-02 6.94e+03 1.57e+02 bond pdb=" C11 F86 G 4 " pdb=" N5 F86 G 4 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C3 F86 G 4 " pdb=" C4 F86 G 4 " ideal model delta sigma weight residual 1.526 1.670 -0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" O7 F86 G 4 " pdb=" P1 F86 G 4 " ideal model delta sigma weight residual 1.491 1.649 -0.158 1.70e-02 3.46e+03 8.66e+01 ... (remaining 10980 not shown) Histogram of bond angle deviations from ideal: 82.08 - 101.65: 69 101.65 - 121.21: 12237 121.21 - 140.78: 2742 140.78 - 160.35: 0 160.35 - 179.91: 1 Bond angle restraints: 15049 Sorted by residual: angle pdb=" O2' C F -2 " pdb=" C2' C F -2 " pdb=" C1' C F -2 " ideal model delta sigma weight residual 108.40 82.08 26.32 1.50e+00 4.44e-01 3.08e+02 angle pdb=" C12 F86 G 4 " pdb=" N2 F86 G 4 " pdb=" N1 F86 G 4 " ideal model delta sigma weight residual 111.53 121.71 -10.18 1.00e+00 1.00e+00 1.04e+02 angle pdb=" N2 F86 G 4 " pdb=" C12 F86 G 4 " pdb=" N4 F86 G 4 " ideal model delta sigma weight residual 128.74 120.63 8.11 1.17e+00 7.33e-01 4.82e+01 angle pdb=" C3' C F -2 " pdb=" C2' C F -2 " pdb=" O2' C F -2 " ideal model delta sigma weight residual 110.70 119.92 -9.22 1.50e+00 4.44e-01 3.78e+01 angle pdb=" C9 F86 G 4 " pdb=" N1 F86 G 4 " pdb=" N2 F86 G 4 " ideal model delta sigma weight residual 124.86 119.91 4.95 1.00e+00 1.00e+00 2.45e+01 ... (remaining 15044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5832 17.75 - 35.50: 542 35.50 - 53.26: 79 53.26 - 71.01: 17 71.01 - 88.76: 7 Dihedral angle restraints: 6477 sinusoidal: 2749 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TRP D 182 " pdb=" C TRP D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 143.54 36.46 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP A 109 " pdb=" C ASP A 109 " pdb=" N MET A 110 " pdb=" CA MET A 110 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1468 0.060 - 0.120: 229 0.120 - 0.180: 18 0.180 - 0.239: 3 0.239 - 0.299: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" P C F -3 " pdb=" OP1 C F -3 " pdb=" OP2 C F -3 " pdb=" O5' C F -3 " both_signs ideal model delta sigma weight residual True 2.41 -2.11 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB THR A 120 " pdb=" CA THR A 120 " pdb=" OG1 THR A 120 " pdb=" CG2 THR A 120 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3 F86 G 4 " pdb=" C2 F86 G 4 " pdb=" C4 F86 G 4 " pdb=" O3 F86 G 4 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1717 not shown) Planarity restraints: 1807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO D 183 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C F -2 " 0.040 2.00e-02 2.50e+03 2.09e-02 9.78e+00 pdb=" N1 C F -2 " -0.042 2.00e-02 2.50e+03 pdb=" C2 C F -2 " -0.014 2.00e-02 2.50e+03 pdb=" O2 C F -2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C F -2 " 0.011 2.00e-02 2.50e+03 pdb=" C4 C F -2 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C F -2 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C F -2 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F -2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F -3 " 0.015 2.00e-02 2.50e+03 1.69e-02 6.39e+00 pdb=" N1 C F -3 " -0.022 2.00e-02 2.50e+03 pdb=" C2 C F -3 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C F -3 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C F -3 " 0.022 2.00e-02 2.50e+03 pdb=" C4 C F -3 " -0.033 2.00e-02 2.50e+03 pdb=" N4 C F -3 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C F -3 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C F -3 " 0.006 2.00e-02 2.50e+03 ... (remaining 1804 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2579 2.78 - 3.31: 9587 3.31 - 3.84: 17879 3.84 - 4.37: 22257 4.37 - 4.90: 37013 Nonbonded interactions: 89315 Sorted by model distance: nonbonded pdb=" OD2 ASP A 170 " pdb=" NH2 ARG A 173 " model vdw 2.256 2.520 nonbonded pdb=" O SER C 54 " pdb=" OG SER C 57 " model vdw 2.291 2.440 nonbonded pdb=" NH2 ARG A 279 " pdb=" OG SER A 318 " model vdw 2.302 2.520 nonbonded pdb=" O SER D 151 " pdb=" OG SER D 151 " model vdw 2.305 2.440 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.312 2.440 ... (remaining 89310 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 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.390 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 36.590 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 10985 Z= 0.420 Angle : 0.675 26.321 15049 Z= 0.408 Chirality : 0.044 0.299 1720 Planarity : 0.004 0.083 1807 Dihedral : 13.790 88.760 4065 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1246 helix: -1.20 (0.19), residues: 588 sheet: -2.00 (0.39), residues: 129 loop : -2.70 (0.22), residues: 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.085 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 146 average time/residue: 1.3385 time to fit residues: 209.7402 Evaluate side-chains 120 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1409 time to fit residues: 1.8735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 75 HIS A 81 GLN A 99 HIS A 138 ASN A 168 ASN A 312 ASN A 356 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 534 ASN A 613 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS B 140 ASN B 158 GLN B 192 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 105 ASN D 108 ASN D 109 ASN D 140 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10985 Z= 0.188 Angle : 0.513 7.572 15049 Z= 0.266 Chirality : 0.040 0.162 1720 Planarity : 0.004 0.073 1807 Dihedral : 7.152 82.854 1730 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.26 % Allowed : 10.85 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.22), residues: 1246 helix: -0.11 (0.21), residues: 578 sheet: -1.38 (0.42), residues: 127 loop : -2.12 (0.23), residues: 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.096 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 1.1832 time to fit residues: 183.5387 Evaluate side-chains 130 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 9 average time/residue: 0.5987 time to fit residues: 7.7971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN C 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10985 Z= 0.322 Angle : 0.558 8.068 15049 Z= 0.292 Chirality : 0.042 0.170 1720 Planarity : 0.004 0.073 1807 Dihedral : 7.183 77.418 1730 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.17 % Allowed : 13.38 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1246 helix: -0.09 (0.21), residues: 596 sheet: -1.03 (0.43), residues: 132 loop : -2.12 (0.24), residues: 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.169 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 134 average time/residue: 1.2493 time to fit residues: 181.1309 Evaluate side-chains 125 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 4 average time/residue: 0.1424 time to fit residues: 2.4608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN C 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10985 Z= 0.131 Angle : 0.464 7.368 15049 Z= 0.243 Chirality : 0.038 0.147 1720 Planarity : 0.003 0.063 1807 Dihedral : 6.917 76.237 1730 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.72 % Allowed : 15.28 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1246 helix: 0.36 (0.22), residues: 578 sheet: -0.69 (0.45), residues: 126 loop : -1.84 (0.24), residues: 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.159 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 152 average time/residue: 1.1689 time to fit residues: 193.0036 Evaluate side-chains 137 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.1535 time to fit residues: 2.3133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 705 ASN A 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10985 Z= 0.145 Angle : 0.475 8.468 15049 Z= 0.245 Chirality : 0.038 0.146 1720 Planarity : 0.003 0.061 1807 Dihedral : 6.785 74.150 1730 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.81 % Allowed : 15.55 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.23), residues: 1246 helix: 0.50 (0.22), residues: 579 sheet: -0.36 (0.45), residues: 131 loop : -1.69 (0.25), residues: 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.229 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 144 average time/residue: 1.1946 time to fit residues: 188.0168 Evaluate side-chains 132 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.1378 time to fit residues: 2.1666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 57 GLN A 138 ASN A 497 ASN A 734 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10985 Z= 0.128 Angle : 0.463 7.705 15049 Z= 0.238 Chirality : 0.038 0.143 1720 Planarity : 0.003 0.056 1807 Dihedral : 6.667 72.408 1730 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.99 % Allowed : 16.46 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.57 (0.24), residues: 1246 helix: 0.64 (0.22), residues: 579 sheet: -0.22 (0.45), residues: 131 loop : -1.54 (0.25), residues: 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.063 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 141 average time/residue: 1.1776 time to fit residues: 180.4838 Evaluate side-chains 132 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 2 average time/residue: 0.1885 time to fit residues: 2.3137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10985 Z= 0.137 Angle : 0.466 7.247 15049 Z= 0.238 Chirality : 0.038 0.142 1720 Planarity : 0.003 0.055 1807 Dihedral : 6.610 70.741 1730 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.17 % Allowed : 17.09 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.45 (0.24), residues: 1246 helix: 0.73 (0.22), residues: 579 sheet: -0.14 (0.46), residues: 126 loop : -1.46 (0.25), residues: 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.181 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 139 average time/residue: 1.1952 time to fit residues: 180.5340 Evaluate side-chains 135 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 3 average time/residue: 1.1276 time to fit residues: 5.1752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 chunk 82 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 138 ASN A 497 ASN A 568 ASN A 734 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10985 Z= 0.233 Angle : 0.514 9.400 15049 Z= 0.264 Chirality : 0.040 0.146 1720 Planarity : 0.003 0.056 1807 Dihedral : 6.788 69.239 1730 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.26 % Allowed : 17.36 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.56 (0.24), residues: 1246 helix: 0.56 (0.22), residues: 586 sheet: -0.15 (0.44), residues: 132 loop : -1.47 (0.26), residues: 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.140 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 1.2074 time to fit residues: 188.6049 Evaluate side-chains 137 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 2 average time/residue: 0.1278 time to fit residues: 2.0358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.0010 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 734 ASN C 31 GLN D 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10985 Z= 0.143 Angle : 0.474 7.483 15049 Z= 0.244 Chirality : 0.038 0.142 1720 Planarity : 0.003 0.053 1807 Dihedral : 6.653 69.125 1730 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 18.17 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.37 (0.24), residues: 1246 helix: 0.75 (0.22), residues: 579 sheet: -0.11 (0.46), residues: 126 loop : -1.37 (0.26), residues: 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.217 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 140 average time/residue: 1.1804 time to fit residues: 179.8998 Evaluate side-chains 132 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 1 average time/residue: 0.1444 time to fit residues: 1.8445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10985 Z= 0.241 Angle : 0.529 9.295 15049 Z= 0.273 Chirality : 0.040 0.180 1720 Planarity : 0.004 0.056 1807 Dihedral : 6.757 68.091 1730 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.63 % Allowed : 18.72 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.24), residues: 1246 helix: 0.57 (0.22), residues: 586 sheet: -0.12 (0.45), residues: 132 loop : -1.41 (0.26), residues: 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.061 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 1.2256 time to fit residues: 172.8059 Evaluate side-chains 127 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 1 average time/residue: 0.1415 time to fit residues: 1.7869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092720 restraints weight = 13401.670| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.92 r_work: 0.2952 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10985 Z= 0.156 Angle : 0.489 8.154 15049 Z= 0.254 Chirality : 0.039 0.165 1720 Planarity : 0.003 0.052 1807 Dihedral : 6.687 68.533 1730 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.45 % Allowed : 18.63 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.39 (0.24), residues: 1246 helix: 0.71 (0.22), residues: 582 sheet: -0.05 (0.45), residues: 132 loop : -1.39 (0.26), residues: 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3703.27 seconds wall clock time: 66 minutes 32.97 seconds (3992.97 seconds total)