Starting phenix.real_space_refine on Wed Feb 14 18:34:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfh_30664/02_2024/7dfh_30664_updated.pdb" } resolution = 2.97 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= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 25 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 6263 2.51 5 N 1670 2.21 5 O 1947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 804": "OD1" <-> "OD2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "G ASP 112": "OD1" <-> "OD2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9980 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7328 Classifications: {'peptide': 908} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 877} Chain breaks: 2 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 485 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "P" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "T" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 23 Unusual residues: {' MG': 3, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 301 43.076 63.750 43.645 1.00 48.76 S ATOM 2470 SG CYS A 306 43.499 62.702 39.750 1.00 43.75 S ATOM 2502 SG CYS A 310 46.486 62.891 42.457 1.00 37.28 S ATOM 3910 SG CYS A 487 24.799 59.648 51.489 1.00 53.98 S ATOM 5163 SG CYS A 645 23.650 59.141 47.723 1.00 59.72 S ATOM 5169 SG CYS A 646 26.717 61.845 49.340 1.00 57.57 S Time building chain proxies: 5.90, per 1000 atoms: 0.59 Number of scatterers: 9980 At special positions: 0 Unit cell: (102.624, 93.003, 130.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 25 15.00 Mg 3 11.99 O 1947 8.00 N 1670 7.00 C 6263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 10 sheets defined 42.1% alpha, 11.5% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.856A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.715A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (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 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.966A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 199 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: 4.119A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.395A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (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: 3.850A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.002A 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 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 446 through 458 removed outlier: 4.448A pdb=" N ALA A 449 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.839A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (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: 4.479A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.892A 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 628 through 641 removed outlier: 4.494A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.582A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 852 through 865 removed outlier: 4.438A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 869 No H-bonds generated for 'chain 'A' and resid 867 through 869' Processing helix chain 'A' and resid 875 through 894 removed outlier: 4.233A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 922 No H-bonds generated for 'chain 'A' and resid 919 through 922' Processing helix chain 'B' and resid 79 through 97 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.807A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.905A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.948A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.937A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'G' and resid 86 through 98 Processing helix chain 'G' and resid 101 through 112 Processing helix chain 'G' and resid 135 through 141 Processing helix chain 'G' and resid 174 through 176 No H-bonds generated for 'chain 'G' and resid 174 through 176' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.408A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 104 Processing sheet with id= D, first strand: chain 'A' and resid 330 through 335 removed outlier: 3.513A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.783A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.859A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.678A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.445A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 127 through 132 364 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2541 1.33 - 1.45: 2117 1.45 - 1.57: 5426 1.57 - 1.69: 42 1.69 - 1.81: 105 Bond restraints: 10231 Sorted by residual: bond pdb=" O5' RVP P1201 " pdb=" P RVP P1201 " ideal model delta sigma weight residual 1.593 1.293 0.300 1.50e-02 4.44e+03 3.99e+02 bond pdb=" C5' RVP P1201 " pdb=" O5' RVP P1201 " ideal model delta sigma weight residual 1.420 1.641 -0.221 1.50e-02 4.44e+03 2.16e+02 bond pdb=" P G P 20 " pdb=" O5' G P 20 " ideal model delta sigma weight residual 1.593 1.389 0.204 1.50e-02 4.44e+03 1.84e+02 bond pdb=" C6 RVP P1201 " pdb=" N1 RVP P1201 " ideal model delta sigma weight residual 1.452 1.322 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C4' RVP P1201 " pdb=" C5' RVP P1201 " ideal model delta sigma weight residual 1.508 1.447 0.061 1.50e-02 4.44e+03 1.68e+01 ... (remaining 10226 not shown) Histogram of bond angle deviations from ideal: 93.26 - 101.46: 47 101.46 - 109.67: 1428 109.67 - 117.87: 6233 117.87 - 126.08: 6098 126.08 - 134.28: 177 Bond angle restraints: 13983 Sorted by residual: angle pdb=" C5' RVP P1201 " pdb=" C4' RVP P1201 " pdb=" O4' RVP P1201 " ideal model delta sigma weight residual 109.80 124.68 -14.88 1.50e+00 4.44e-01 9.84e+01 angle pdb=" C3' RVP P1201 " pdb=" C4' RVP P1201 " pdb=" C5' RVP P1201 " ideal model delta sigma weight residual 116.00 102.83 13.17 1.50e+00 4.44e-01 7.71e+01 angle pdb=" C4' U P 17 " pdb=" C3' U P 17 " pdb=" O3' U P 17 " ideal model delta sigma weight residual 113.00 125.52 -12.52 1.50e+00 4.44e-01 6.97e+01 angle pdb=" O2P RVP P1201 " pdb=" P RVP P1201 " pdb=" O5' RVP P1201 " ideal model delta sigma weight residual 108.00 126.70 -18.70 3.00e+00 1.11e-01 3.89e+01 angle pdb=" P G P 20 " pdb=" O5' G P 20 " pdb=" C5' G P 20 " ideal model delta sigma weight residual 120.90 129.72 -8.82 1.50e+00 4.44e-01 3.46e+01 ... (remaining 13978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 5387 16.99 - 33.99: 579 33.99 - 50.98: 105 50.98 - 67.97: 26 67.97 - 84.97: 18 Dihedral angle restraints: 6115 sinusoidal: 2582 harmonic: 3533 Sorted by residual: dihedral pdb=" CA ARG A 914 " pdb=" C ARG A 914 " pdb=" N TYR A 915 " pdb=" CA TYR A 915 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ASP B 99 " pdb=" C ASP B 99 " pdb=" N ASN B 100 " pdb=" CA ASN B 100 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 6112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1323 0.071 - 0.142: 233 0.142 - 0.213: 32 0.213 - 0.284: 3 0.284 - 0.355: 2 Chirality restraints: 1593 Sorted by residual: chirality pdb=" P G P 20 " pdb=" OP1 G P 20 " pdb=" OP2 G P 20 " pdb=" O5' G P 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' U P 17 " pdb=" C4' U P 17 " pdb=" O3' U P 17 " pdb=" C2' U P 17 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB VAL C 53 " pdb=" CA VAL C 53 " pdb=" CG1 VAL C 53 " pdb=" CG2 VAL C 53 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1590 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U P 17 " 0.040 2.00e-02 2.50e+03 2.25e-02 1.14e+01 pdb=" N1 U P 17 " -0.050 2.00e-02 2.50e+03 pdb=" C2 U P 17 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U P 17 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U P 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U P 17 " 0.020 2.00e-02 2.50e+03 pdb=" O4 U P 17 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U P 17 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U P 17 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.038 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO B 178 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 243 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.030 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1797 2.76 - 3.29: 8860 3.29 - 3.83: 17172 3.83 - 4.36: 20696 4.36 - 4.90: 34691 Nonbonded interactions: 83216 Sorted by model distance: nonbonded pdb=" NZ LYS A 577 " pdb=" OP1 C T 13 " model vdw 2.224 2.520 nonbonded pdb=" CA ASP A 618 " pdb=" O HOH A1102 " model vdw 2.232 3.470 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.269 2.440 nonbonded pdb=" O THR G 137 " pdb=" OG1 THR G 141 " model vdw 2.287 2.440 nonbonded pdb=" N2 G P 13 " pdb=" O2 C T 18 " model vdw 2.290 2.496 ... (remaining 83211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 179 or resid 182 through 191)) selection = chain 'G' } 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: 1.250 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: 4.250 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 34.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.008 0.300 10231 Z= 0.458 Angle : 0.934 18.703 13983 Z= 0.541 Chirality : 0.055 0.355 1593 Planarity : 0.006 0.056 1708 Dihedral : 15.076 84.965 3829 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % 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: -3.16 (0.20), residues: 1177 helix: -2.63 (0.16), residues: 523 sheet: -1.03 (0.42), residues: 142 loop : -1.63 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 509 HIS 0.011 0.001 HIS C 36 PHE 0.022 0.002 PHE A 348 TYR 0.018 0.002 TYR G 149 ARG 0.005 0.001 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.029 Fit side-chains REVERT: A 81 GLN cc_start: 0.7377 (tt0) cc_final: 0.7151 (tm-30) REVERT: A 98 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7573 (tttp) REVERT: A 105 ARG cc_start: 0.6738 (mtp-110) cc_final: 0.6416 (mtp-110) REVERT: A 197 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7535 (ttp80) REVERT: A 289 TYR cc_start: 0.7869 (m-80) cc_final: 0.7493 (m-80) REVERT: A 794 MET cc_start: 0.8715 (ttp) cc_final: 0.8369 (ttp) REVERT: A 855 MET cc_start: 0.6997 (mtm) cc_final: 0.6535 (mtp) REVERT: C 18 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8364 (tm130) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 1.0288 time to fit residues: 218.7473 Evaluate side-chains 148 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 75 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 177 ASN A 191 GLN A 256 HIS A 491 ASN A 570 GLN A 573 GLN A 613 HIS A 642 HIS A 705 ASN A 790 ASN A 791 ASN A 815 GLN A 892 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 140 ASN C 31 GLN C 36 HIS C 37 ASN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10231 Z= 0.270 Angle : 0.554 7.677 13983 Z= 0.298 Chirality : 0.043 0.151 1593 Planarity : 0.004 0.037 1708 Dihedral : 10.801 74.039 1616 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.12 % Allowed : 13.07 % Favored : 83.81 % 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: -1.60 (0.22), residues: 1177 helix: -1.05 (0.20), residues: 537 sheet: -0.66 (0.43), residues: 142 loop : -0.99 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 182 HIS 0.010 0.001 HIS A 892 PHE 0.015 0.001 PHE A 326 TYR 0.016 0.001 TYR A 606 ARG 0.004 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 794 MET cc_start: 0.8754 (ttp) cc_final: 0.8350 (ttp) REVERT: A 855 MET cc_start: 0.7024 (mtm) cc_final: 0.6741 (mtm) REVERT: C 18 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8408 (tm130) REVERT: G 184 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6213 (pt) outliers start: 33 outliers final: 10 residues processed: 181 average time/residue: 0.9917 time to fit residues: 196.1342 Evaluate side-chains 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 140 ASN C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10231 Z= 0.149 Angle : 0.488 7.214 13983 Z= 0.261 Chirality : 0.040 0.149 1593 Planarity : 0.003 0.026 1708 Dihedral : 10.435 73.666 1616 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.37 % Allowed : 15.81 % Favored : 81.82 % 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: -0.82 (0.23), residues: 1177 helix: -0.27 (0.22), residues: 531 sheet: -0.50 (0.42), residues: 142 loop : -0.68 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 182 HIS 0.004 0.001 HIS C 36 PHE 0.010 0.001 PHE A 652 TYR 0.013 0.001 TYR A 156 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.146 Fit side-chains REVERT: A 197 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7605 (ttp80) REVERT: A 289 TYR cc_start: 0.7873 (m-80) cc_final: 0.7429 (m-80) REVERT: A 664 SER cc_start: 0.8119 (m) cc_final: 0.7825 (p) REVERT: A 794 MET cc_start: 0.8713 (ttp) cc_final: 0.8327 (ttp) REVERT: A 855 MET cc_start: 0.7011 (mtm) cc_final: 0.6560 (mtm) REVERT: A 859 PHE cc_start: 0.8560 (m-80) cc_final: 0.8296 (m-80) outliers start: 25 outliers final: 9 residues processed: 173 average time/residue: 0.9994 time to fit residues: 188.9413 Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain G residue 169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10231 Z= 0.289 Angle : 0.540 6.667 13983 Z= 0.286 Chirality : 0.043 0.174 1593 Planarity : 0.003 0.025 1708 Dihedral : 10.382 73.854 1616 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.50 % Allowed : 17.05 % Favored : 79.45 % 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: -0.46 (0.24), residues: 1177 helix: 0.09 (0.23), residues: 526 sheet: -0.36 (0.42), residues: 141 loop : -0.56 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 182 HIS 0.006 0.001 HIS C 36 PHE 0.015 0.002 PHE A 859 TYR 0.016 0.001 TYR A 156 ARG 0.002 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 1.029 Fit side-chains REVERT: A 370 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: A 794 MET cc_start: 0.8829 (ttp) cc_final: 0.8399 (ttp) REVERT: A 855 MET cc_start: 0.7004 (mtm) cc_final: 0.6676 (mtm) REVERT: G 189 LEU cc_start: 0.7068 (mm) cc_final: 0.6453 (pp) outliers start: 37 outliers final: 17 residues processed: 167 average time/residue: 0.9307 time to fit residues: 170.5055 Evaluate side-chains 160 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10231 Z= 0.144 Angle : 0.488 6.995 13983 Z= 0.257 Chirality : 0.041 0.159 1593 Planarity : 0.003 0.025 1708 Dihedral : 10.265 73.757 1616 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.27 % Allowed : 18.75 % Favored : 78.98 % 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: -0.13 (0.24), residues: 1177 helix: 0.39 (0.23), residues: 525 sheet: -0.32 (0.42), residues: 141 loop : -0.38 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 182 HIS 0.003 0.000 HIS C 36 PHE 0.010 0.001 PHE A 652 TYR 0.012 0.001 TYR A 156 ARG 0.004 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.061 Fit side-chains REVERT: A 370 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: A 794 MET cc_start: 0.8769 (ttp) cc_final: 0.8361 (ttp) REVERT: A 855 MET cc_start: 0.6937 (mtm) cc_final: 0.6531 (mtm) REVERT: A 859 PHE cc_start: 0.8487 (m-80) cc_final: 0.8226 (m-80) outliers start: 24 outliers final: 8 residues processed: 171 average time/residue: 0.9276 time to fit residues: 174.4244 Evaluate side-chains 153 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10231 Z= 0.289 Angle : 0.549 7.401 13983 Z= 0.289 Chirality : 0.044 0.168 1593 Planarity : 0.003 0.024 1708 Dihedral : 10.330 73.856 1616 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.03 % Allowed : 18.84 % Favored : 78.12 % 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: -0.22 (0.24), residues: 1177 helix: 0.28 (0.23), residues: 532 sheet: -0.46 (0.41), residues: 142 loop : -0.34 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 182 HIS 0.006 0.001 HIS C 36 PHE 0.015 0.002 PHE A 859 TYR 0.019 0.001 TYR A 289 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.111 Fit side-chains REVERT: A 370 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: A 666 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7422 (ttm) REVERT: A 794 MET cc_start: 0.8847 (ttp) cc_final: 0.8394 (ttp) REVERT: A 855 MET cc_start: 0.6982 (mtm) cc_final: 0.6725 (mtp) REVERT: A 859 PHE cc_start: 0.8580 (m-80) cc_final: 0.8322 (m-80) REVERT: G 98 LEU cc_start: 0.7128 (mm) cc_final: 0.6662 (mm) REVERT: G 189 LEU cc_start: 0.7018 (mm) cc_final: 0.6553 (pp) outliers start: 32 outliers final: 15 residues processed: 171 average time/residue: 0.9177 time to fit residues: 172.4624 Evaluate side-chains 163 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10231 Z= 0.158 Angle : 0.497 8.477 13983 Z= 0.261 Chirality : 0.041 0.172 1593 Planarity : 0.003 0.024 1708 Dihedral : 10.276 73.740 1616 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.56 % Allowed : 19.51 % Favored : 77.94 % 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: -0.09 (0.24), residues: 1177 helix: 0.40 (0.23), residues: 539 sheet: -0.38 (0.42), residues: 142 loop : -0.30 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 182 HIS 0.002 0.000 HIS C 36 PHE 0.009 0.001 PHE A 652 TYR 0.018 0.001 TYR A 289 ARG 0.002 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.163 Fit side-chains REVERT: A 370 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: A 794 MET cc_start: 0.8808 (ttp) cc_final: 0.8404 (ttp) REVERT: A 855 MET cc_start: 0.6905 (mtm) cc_final: 0.6630 (mtp) REVERT: A 859 PHE cc_start: 0.8470 (m-80) cc_final: 0.8206 (m-80) REVERT: G 189 LEU cc_start: 0.7003 (mm) cc_final: 0.6478 (pp) outliers start: 27 outliers final: 14 residues processed: 167 average time/residue: 0.9565 time to fit residues: 175.7144 Evaluate side-chains 157 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 0.0270 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.0000 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10231 Z= 0.116 Angle : 0.489 9.149 13983 Z= 0.253 Chirality : 0.040 0.164 1593 Planarity : 0.003 0.024 1708 Dihedral : 10.129 73.812 1616 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.70 % Allowed : 20.55 % Favored : 77.75 % 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: 0.11 (0.24), residues: 1177 helix: 0.54 (0.23), residues: 545 sheet: -0.30 (0.42), residues: 140 loop : -0.16 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.002 0.000 HIS C 36 PHE 0.009 0.001 PHE A 77 TYR 0.013 0.001 TYR A 289 ARG 0.001 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.168 Fit side-chains REVERT: A 40 ASP cc_start: 0.7022 (p0) cc_final: 0.6775 (p0) REVERT: A 197 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7851 (ttp80) REVERT: A 370 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: A 664 SER cc_start: 0.7918 (m) cc_final: 0.7415 (p) REVERT: A 794 MET cc_start: 0.8744 (ttp) cc_final: 0.8387 (ttp) REVERT: A 855 MET cc_start: 0.6819 (mtm) cc_final: 0.6453 (mtm) REVERT: A 859 PHE cc_start: 0.8410 (m-80) cc_final: 0.8189 (m-80) REVERT: G 189 LEU cc_start: 0.6983 (mm) cc_final: 0.6450 (pp) outliers start: 18 outliers final: 6 residues processed: 176 average time/residue: 0.9996 time to fit residues: 192.4205 Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN B 168 GLN C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10231 Z= 0.151 Angle : 0.504 13.079 13983 Z= 0.260 Chirality : 0.041 0.164 1593 Planarity : 0.003 0.023 1708 Dihedral : 10.097 73.798 1616 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.61 % Allowed : 22.06 % Favored : 76.33 % 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: 0.28 (0.25), residues: 1177 helix: 0.73 (0.23), residues: 532 sheet: -0.27 (0.42), residues: 140 loop : -0.11 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.027 0.001 PHE A 396 TYR 0.018 0.001 TYR B 138 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.085 Fit side-chains REVERT: A 40 ASP cc_start: 0.6994 (p0) cc_final: 0.6742 (p0) REVERT: A 77 PHE cc_start: 0.8174 (t80) cc_final: 0.7916 (t80) REVERT: A 370 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: A 664 SER cc_start: 0.7929 (m) cc_final: 0.7420 (p) REVERT: A 794 MET cc_start: 0.8798 (ttp) cc_final: 0.8394 (ttp) REVERT: A 855 MET cc_start: 0.6820 (mtm) cc_final: 0.6334 (mtm) REVERT: A 859 PHE cc_start: 0.8439 (m-80) cc_final: 0.8228 (m-80) REVERT: G 129 MET cc_start: 0.7466 (mtp) cc_final: 0.6604 (mmt) REVERT: G 189 LEU cc_start: 0.7003 (mm) cc_final: 0.6465 (pp) outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 0.9156 time to fit residues: 163.4591 Evaluate side-chains 156 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain C residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10231 Z= 0.161 Angle : 0.522 15.716 13983 Z= 0.267 Chirality : 0.041 0.166 1593 Planarity : 0.003 0.023 1708 Dihedral : 10.081 73.778 1616 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.61 % Allowed : 21.88 % Favored : 76.52 % 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: 0.29 (0.25), residues: 1177 helix: 0.69 (0.23), residues: 532 sheet: -0.20 (0.42), residues: 142 loop : -0.07 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.026 0.001 PHE A 396 TYR 0.015 0.001 TYR A 289 ARG 0.002 0.000 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.035 Fit side-chains REVERT: A 40 ASP cc_start: 0.6924 (p0) cc_final: 0.6646 (p0) REVERT: A 370 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: A 664 SER cc_start: 0.7894 (m) cc_final: 0.7373 (p) REVERT: A 794 MET cc_start: 0.8804 (ttp) cc_final: 0.8422 (ttp) REVERT: A 821 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7990 (ttpp) REVERT: A 855 MET cc_start: 0.6866 (mtm) cc_final: 0.6597 (mtp) REVERT: A 859 PHE cc_start: 0.8444 (m-80) cc_final: 0.8233 (m-80) REVERT: G 129 MET cc_start: 0.7507 (mtp) cc_final: 0.6637 (mmt) REVERT: G 189 LEU cc_start: 0.6991 (mm) cc_final: 0.6457 (pp) outliers start: 17 outliers final: 11 residues processed: 162 average time/residue: 1.0009 time to fit residues: 180.3930 Evaluate side-chains 160 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115079 restraints weight = 13246.233| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.98 r_work: 0.3341 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10231 Z= 0.157 Angle : 0.508 11.844 13983 Z= 0.262 Chirality : 0.041 0.174 1593 Planarity : 0.003 0.023 1708 Dihedral : 10.051 73.758 1616 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 22.44 % Favored : 76.04 % 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: 0.36 (0.25), residues: 1177 helix: 0.75 (0.23), residues: 531 sheet: -0.20 (0.42), residues: 142 loop : -0.02 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.028 0.001 PHE A 396 TYR 0.015 0.001 TYR A 289 ARG 0.001 0.000 ARG A 735 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.37 seconds wall clock time: 66 minutes 40.93 seconds (4000.93 seconds total)