Starting phenix.real_space_refine (version: dev) on Sat Feb 18 16:22:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/02_2023/8h8a_34540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/02_2023/8h8a_34540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/02_2023/8h8a_34540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/02_2023/8h8a_34540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/02_2023/8h8a_34540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8a_34540/02_2023/8h8a_34540.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ASP 153": "OD1" <-> "OD2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "B GLU 1134": "OE1" <-> "OE2" Residue "B GLU 1146": "OE1" <-> "OE2" Residue "B GLU 1163": "OE1" <-> "OE2" Residue "B GLU 1193": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8454 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7844 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Time building chain proxies: 5.09, per 1000 atoms: 0.60 Number of scatterers: 8454 At special positions: 0 Unit cell: (87.87, 79.17, 113.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1657 8.00 N 1468 7.00 C 5317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 15 sheets defined 2.6% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.073A pdb=" N SER A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 384 " --> pdb=" O GLY A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 384' Processing helix chain 'B' and resid 1139 through 1148 Processing helix chain 'B' and resid 1154 through 1165 removed outlier: 3.645A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 170 removed outlier: 3.610A pdb=" N LEU A 166 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.438A pdb=" N ARG A 266 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL A 279 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 268 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 275 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.463A pdb=" N ILE A 298 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS A 310 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 300 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 311 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 320 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.642A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 403 removed outlier: 5.118A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN A 464 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 469 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 493 removed outlier: 4.038A pdb=" N TYR A 504 " --> pdb=" O TRP A 513 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP A 513 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN A 506 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG A 511 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 523 through 526 removed outlier: 5.545A pdb=" N VAL A 533 " --> pdb=" O TRP A 545 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 555 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 587 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A 596 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR A 599 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR A 608 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP A 656 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 661 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N ASN A 660 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N TYR A 676 " --> pdb=" O ASN A 660 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR A 662 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 673 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A 685 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP A 675 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 696 through 697 removed outlier: 7.088A pdb=" N LYS A 696 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 715 through 717 removed outlier: 5.530A pdb=" N GLN A 724 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 769 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 781 removed outlier: 3.849A pdb=" N GLU A 780 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 791 through 792 removed outlier: 3.693A pdb=" N THR A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 810 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 821 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 926 through 927 removed outlier: 3.797A pdb=" N LYS A 942 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL A 941 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A 961 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR A 981 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU A 995 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 999 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 11.680A pdb=" N ARG A 998 " --> pdb=" O TYR A1013 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR A1013 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A1000 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE A1008 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A1025 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP A1010 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A1023 " --> pdb=" O TRP A1010 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A1012 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A1021 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU A1041 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A1054 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N VAL A1051 " --> pdb=" O GLU A1067 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU A1067 " --> pdb=" O VAL A1051 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A1053 " --> pdb=" O ASP A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1079 through 1080 Processing sheet with id=AB6, first strand: chain 'A' and resid 1125 through 1126 211 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2841 1.34 - 1.46: 1982 1.46 - 1.58: 3813 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 8652 Sorted by residual: bond pdb=" CA TYR B1214 " pdb=" CB TYR B1214 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.22e-02 2.03e+03 2.21e+00 bond pdb=" CA LEU A 204 " pdb=" C LEU A 204 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.22e-02 6.72e+03 1.47e+00 bond pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.39e+00 bond pdb=" CA ALA A 151 " pdb=" C ALA A 151 " ideal model delta sigma weight residual 1.523 1.509 0.014 1.30e-02 5.92e+03 1.24e+00 bond pdb=" CB ASP A 719 " pdb=" CG ASP A 719 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 ... (remaining 8647 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.48: 225 107.48 - 114.10: 4601 114.10 - 120.72: 3474 120.72 - 127.35: 3323 127.35 - 133.97: 81 Bond angle restraints: 11704 Sorted by residual: angle pdb=" N GLU A 203 " pdb=" CA GLU A 203 " pdb=" C GLU A 203 " ideal model delta sigma weight residual 107.61 115.32 -7.71 1.74e+00 3.30e-01 1.96e+01 angle pdb=" N VAL A 342 " pdb=" CA VAL A 342 " pdb=" C VAL A 342 " ideal model delta sigma weight residual 113.10 108.88 4.22 9.70e-01 1.06e+00 1.89e+01 angle pdb=" N GLY A 152 " pdb=" CA GLY A 152 " pdb=" C GLY A 152 " ideal model delta sigma weight residual 112.51 106.32 6.19 1.53e+00 4.27e-01 1.64e+01 angle pdb=" N VAL B1179 " pdb=" CA VAL B1179 " pdb=" C VAL B1179 " ideal model delta sigma weight residual 113.47 109.55 3.92 1.01e+00 9.80e-01 1.51e+01 angle pdb=" N VAL A 708 " pdb=" CA VAL A 708 " pdb=" C VAL A 708 " ideal model delta sigma weight residual 110.21 106.90 3.31 1.13e+00 7.83e-01 8.59e+00 ... (remaining 11699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4668 17.63 - 35.26: 304 35.26 - 52.89: 76 52.89 - 70.52: 14 70.52 - 88.15: 9 Dihedral angle restraints: 5071 sinusoidal: 2057 harmonic: 3014 Sorted by residual: dihedral pdb=" CA ASP A 153 " pdb=" C ASP A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP A 935 " pdb=" CB ASP A 935 " pdb=" CG ASP A 935 " pdb=" OD1 ASP A 935 " ideal model delta sinusoidal sigma weight residual -30.00 -88.49 58.49 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASN A 251 " pdb=" C ASN A 251 " pdb=" N PRO A 252 " pdb=" CA PRO A 252 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 772 0.030 - 0.060: 286 0.060 - 0.089: 68 0.089 - 0.119: 67 0.119 - 0.149: 8 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CA ASP A 719 " pdb=" N ASP A 719 " pdb=" C ASP A 719 " pdb=" CB ASP A 719 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE A1107 " pdb=" N ILE A1107 " pdb=" C ILE A1107 " pdb=" CB ILE A1107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 726 " pdb=" N ILE A 726 " pdb=" C ILE A 726 " pdb=" CB ILE A 726 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1198 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 153 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 154 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 154 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 154 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 625 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 626 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 794 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ASP A 794 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP A 794 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS A 795 " -0.007 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2680 2.82 - 3.34: 6382 3.34 - 3.86: 13029 3.86 - 4.38: 14856 4.38 - 4.90: 26999 Nonbonded interactions: 63946 Sorted by model distance: nonbonded pdb=" O LEU A 960 " pdb=" OH TYR A 974 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR A 715 " pdb=" OE1 GLU B1167 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 393 " pdb=" OG SER A 393 " model vdw 2.331 2.440 nonbonded pdb=" OD1 ASP A 455 " pdb=" OG SER A 457 " model vdw 2.340 2.440 nonbonded pdb=" O SER A 683 " pdb=" OG SER A 683 " model vdw 2.348 2.440 ... (remaining 63941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 5317 2.51 5 N 1468 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.330 Check model and map are aligned: 0.120 Process input model: 26.370 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.002 0.033 8652 Z= 0.117 Angle : 0.505 7.711 11704 Z= 0.318 Chirality : 0.040 0.149 1201 Planarity : 0.004 0.115 1544 Dihedral : 12.991 88.149 3165 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.73 % Favored : 91.17 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.22), residues: 1031 helix: -1.89 (1.07), residues: 21 sheet: 0.31 (0.40), residues: 183 loop : -3.13 (0.17), residues: 827 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 192 average time/residue: 0.2845 time to fit residues: 70.9401 Evaluate side-chains 104 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0790 time to fit residues: 2.5334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 357 GLN A 373 HIS A 456 ASN A 460 GLN A 481 GLN A 510 GLN A 622 GLN A 738 HIS A 755 GLN A 772 GLN A 786 GLN A 936 GLN A1014 GLN A1071 ASN A1082 GLN A1117 GLN B1160 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8652 Z= 0.284 Angle : 0.675 7.038 11704 Z= 0.361 Chirality : 0.046 0.177 1201 Planarity : 0.005 0.046 1544 Dihedral : 4.628 26.921 1172 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.03 % Favored : 87.68 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.23), residues: 1031 helix: -0.91 (1.07), residues: 22 sheet: -0.10 (0.40), residues: 210 loop : -2.88 (0.18), residues: 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.217 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 116 average time/residue: 0.2437 time to fit residues: 38.3682 Evaluate side-chains 91 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1168 time to fit residues: 4.3075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 201 GLN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN A1082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8652 Z= 0.201 Angle : 0.580 11.028 11704 Z= 0.307 Chirality : 0.043 0.246 1201 Planarity : 0.004 0.053 1544 Dihedral : 4.350 26.017 1172 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.48 % Favored : 89.43 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.23), residues: 1031 helix: -0.15 (1.17), residues: 22 sheet: 0.12 (0.46), residues: 158 loop : -2.69 (0.18), residues: 851 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.039 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 94 average time/residue: 0.2425 time to fit residues: 31.2091 Evaluate side-chains 74 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0830 time to fit residues: 2.1858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 26 optimal weight: 7.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 481 GLN A 937 GLN A1082 GLN A1087 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 8652 Z= 0.446 Angle : 0.745 9.340 11704 Z= 0.398 Chirality : 0.048 0.184 1201 Planarity : 0.005 0.065 1544 Dihedral : 5.432 29.130 1172 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.84 % Favored : 85.06 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 1031 helix: -0.02 (1.13), residues: 22 sheet: -0.11 (0.42), residues: 183 loop : -2.77 (0.18), residues: 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 1.041 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 90 average time/residue: 0.2537 time to fit residues: 31.2006 Evaluate side-chains 79 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0878 time to fit residues: 3.7615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 1 optimal weight: 0.0870 chunk 74 optimal weight: 0.0370 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN A1082 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8652 Z= 0.122 Angle : 0.538 6.789 11704 Z= 0.286 Chirality : 0.042 0.170 1201 Planarity : 0.003 0.049 1544 Dihedral : 4.362 26.384 1172 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.57 % Favored : 89.33 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.24), residues: 1031 helix: 0.16 (1.16), residues: 23 sheet: 0.64 (0.48), residues: 139 loop : -2.50 (0.18), residues: 869 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.002 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.2277 time to fit residues: 27.7328 Evaluate side-chains 73 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0851 time to fit residues: 1.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8652 Z= 0.332 Angle : 0.659 7.857 11704 Z= 0.352 Chirality : 0.046 0.167 1201 Planarity : 0.005 0.062 1544 Dihedral : 4.972 27.434 1172 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.35 % Favored : 85.55 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 1031 helix: 0.64 (1.15), residues: 22 sheet: 0.06 (0.44), residues: 169 loop : -2.57 (0.18), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.963 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.2381 time to fit residues: 26.4355 Evaluate side-chains 73 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0867 time to fit residues: 2.7620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 937 GLN A1082 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8652 Z= 0.156 Angle : 0.556 6.825 11704 Z= 0.297 Chirality : 0.043 0.164 1201 Planarity : 0.004 0.058 1544 Dihedral : 4.498 26.089 1172 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.83 % Favored : 88.07 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.24), residues: 1031 helix: 0.67 (1.16), residues: 23 sheet: 0.87 (0.51), residues: 122 loop : -2.44 (0.18), residues: 886 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.094 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 0.2357 time to fit residues: 26.4855 Evaluate side-chains 71 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0840 time to fit residues: 1.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 8652 Z= 0.414 Angle : 0.713 8.530 11704 Z= 0.381 Chirality : 0.047 0.179 1201 Planarity : 0.005 0.066 1544 Dihedral : 5.327 28.403 1172 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.62 % Favored : 84.29 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 1031 helix: 0.47 (1.10), residues: 23 sheet: -0.26 (0.43), residues: 169 loop : -2.56 (0.18), residues: 839 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.257 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.2497 time to fit residues: 26.5548 Evaluate side-chains 72 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0929 time to fit residues: 2.5989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 0.0020 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.0270 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 0.0020 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8652 Z= 0.129 Angle : 0.546 7.142 11704 Z= 0.291 Chirality : 0.042 0.168 1201 Planarity : 0.004 0.055 1544 Dihedral : 4.355 26.906 1172 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.57 % Favored : 89.23 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.24), residues: 1031 helix: 0.86 (1.17), residues: 23 sheet: 0.84 (0.53), residues: 113 loop : -2.38 (0.18), residues: 895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.094 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.2546 time to fit residues: 28.6696 Evaluate side-chains 68 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0892 time to fit residues: 1.5997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 8652 Z= 0.356 Angle : 0.687 8.194 11704 Z= 0.367 Chirality : 0.046 0.172 1201 Planarity : 0.005 0.063 1544 Dihedral : 5.103 28.032 1172 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.35 % Favored : 85.55 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.24), residues: 1031 helix: 0.80 (1.14), residues: 23 sheet: -0.09 (0.46), residues: 155 loop : -2.49 (0.18), residues: 853 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.009 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 0.2553 time to fit residues: 23.8133 Evaluate side-chains 59 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0846 time to fit residues: 1.6637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107399 restraints weight = 10905.111| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.16 r_work: 0.3006 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8652 Z= 0.159 Angle : 0.579 7.207 11704 Z= 0.309 Chirality : 0.043 0.162 1201 Planarity : 0.004 0.057 1544 Dihedral : 4.607 27.314 1172 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.93 % Favored : 87.88 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.24), residues: 1031 helix: 1.02 (1.18), residues: 23 sheet: 0.95 (0.51), residues: 122 loop : -2.38 (0.18), residues: 886 =============================================================================== Job complete usr+sys time: 1951.54 seconds wall clock time: 36 minutes 20.60 seconds (2180.60 seconds total)