Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 10:49:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/04_2023/7trd_26086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/04_2023/7trd_26086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/04_2023/7trd_26086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/04_2023/7trd_26086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/04_2023/7trd_26086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trd_26086/04_2023/7trd_26086.pdb" } resolution = 3.3 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= 0.003 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: 5 Type Number sf(0) Gaussians P 224 5.49 5 S 36 5.16 5 C 6931 2.51 5 N 2219 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1097": "NH1" <-> "NH2" Residue "A ARG 1105": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12240 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 21, 'rna3p_pur': 86, 'rna3p_pyr': 96} Link IDs: {'rna2p': 35, 'rna3p': 181} Chain breaks: 2 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7488 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877} Chain breaks: 4 Chain: "N" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 7.44, per 1000 atoms: 0.61 Number of scatterers: 12240 At special positions: 0 Unit cell: (108.9, 122.1, 108.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 224 15.00 O 2830 8.00 N 2219 7.00 C 6931 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: 6.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 55.4% alpha, 15.2% beta 64 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 removed outlier: 3.604A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.839A pdb=" N LEU A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.999A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.574A pdb=" N ALA A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 401 removed outlier: 4.037A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.782A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.781A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.716A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.506A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.655A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 560 removed outlier: 3.764A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.387A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.515A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.531A pdb=" N SER A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.651A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.762A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 765 through 769 removed outlier: 4.006A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.582A pdb=" N PHE A 776 " --> pdb=" O TYR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.789A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 4.052A pdb=" N LEU A 958 " --> pdb=" O ARG A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.120A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.323A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.651A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.508A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.712A pdb=" N ALA A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.601A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.640A pdb=" N VAL A 904 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 712 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS A 902 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930 396 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 332 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 6.35 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: 2612 1.33 - 1.45: 3958 1.45 - 1.57: 5907 1.57 - 1.69: 444 1.69 - 1.81: 47 Bond restraints: 12968 Sorted by residual: bond pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.50e+01 bond pdb=" N VAL A 697 " pdb=" CA VAL A 697 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.11e+00 bond pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.97e+00 bond pdb=" N ASN A 125 " pdb=" CA ASN A 125 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.26e+00 bond pdb=" N GLU A 705 " pdb=" CA GLU A 705 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.28e-02 6.10e+03 6.06e+00 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 1441 106.24 - 113.19: 7292 113.19 - 120.13: 4825 120.13 - 127.08: 4553 127.08 - 134.02: 533 Bond angle restraints: 18644 Sorted by residual: angle pdb=" O LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 122.07 117.19 4.88 1.03e+00 9.43e-01 2.25e+01 angle pdb=" N VAL A 596 " pdb=" CA VAL A 596 " pdb=" C VAL A 596 " ideal model delta sigma weight residual 112.43 108.61 3.82 9.20e-01 1.18e+00 1.73e+01 angle pdb=" CA LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 117.07 121.64 -4.57 1.14e+00 7.69e-01 1.61e+01 angle pdb=" C LYS A 973 " pdb=" N LEU A 974 " pdb=" CA LEU A 974 " ideal model delta sigma weight residual 120.44 125.62 -5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" N ASP A1038 " pdb=" CA ASP A1038 " pdb=" C ASP A1038 " ideal model delta sigma weight residual 113.28 109.10 4.18 1.22e+00 6.72e-01 1.18e+01 ... (remaining 18639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 7011 35.85 - 71.70: 257 71.70 - 107.56: 24 107.56 - 143.41: 4 143.41 - 179.26: 3 Dihedral angle restraints: 7299 sinusoidal: 4576 harmonic: 2723 Sorted by residual: dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual 232.00 52.74 179.26 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual -128.00 48.74 -176.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 291 " pdb=" C1' U B 291 " pdb=" N1 U B 291 " pdb=" C2 U B 291 " ideal model delta sinusoidal sigma weight residual -128.00 40.41 -168.41 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 7296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1913 0.048 - 0.095: 287 0.095 - 0.143: 61 0.143 - 0.190: 22 0.190 - 0.238: 2 Chirality restraints: 2285 Sorted by residual: chirality pdb=" P G B 130 " pdb=" OP1 G B 130 " pdb=" OP2 G B 130 " pdb=" O5' G B 130 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1' A B 174 " pdb=" O4' A B 174 " pdb=" C2' A B 174 " pdb=" N9 A B 174 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' G B 130 " pdb=" C4' G B 130 " pdb=" O3' G B 130 " pdb=" C2' G B 130 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 2282 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 130 " -0.001 2.00e-02 2.50e+03 4.15e-02 5.17e+01 pdb=" N9 G B 130 " 0.002 2.00e-02 2.50e+03 pdb=" C8 G B 130 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G B 130 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 130 " 0.036 2.00e-02 2.50e+03 pdb=" C6 G B 130 " -0.105 2.00e-02 2.50e+03 pdb=" O6 G B 130 " 0.069 2.00e-02 2.50e+03 pdb=" N1 G B 130 " -0.039 2.00e-02 2.50e+03 pdb=" C2 G B 130 " 0.046 2.00e-02 2.50e+03 pdb=" N2 G B 130 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 130 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G B 130 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 129 " 0.003 2.00e-02 2.50e+03 3.20e-02 2.82e+01 pdb=" N9 A B 129 " -0.003 2.00e-02 2.50e+03 pdb=" C8 A B 129 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A B 129 " -0.015 2.00e-02 2.50e+03 pdb=" C5 A B 129 " 0.075 2.00e-02 2.50e+03 pdb=" C6 A B 129 " 0.020 2.00e-02 2.50e+03 pdb=" N6 A B 129 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A B 129 " -0.045 2.00e-02 2.50e+03 pdb=" C2 A B 129 " 0.031 2.00e-02 2.50e+03 pdb=" N3 A B 129 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 129 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 131 " -0.015 2.00e-02 2.50e+03 3.41e-02 2.62e+01 pdb=" N1 C B 131 " -0.012 2.00e-02 2.50e+03 pdb=" C2 C B 131 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C B 131 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C B 131 " 0.007 2.00e-02 2.50e+03 pdb=" C4 C B 131 " 0.077 2.00e-02 2.50e+03 pdb=" N4 C B 131 " -0.064 2.00e-02 2.50e+03 pdb=" C5 C B 131 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C B 131 " 0.001 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1470 2.74 - 3.28: 11066 3.28 - 3.82: 21444 3.82 - 4.36: 24209 4.36 - 4.90: 37863 Nonbonded interactions: 96052 Sorted by model distance: nonbonded pdb=" O LEU A1079 " pdb=" OG1 THR A1083 " model vdw 2.206 2.440 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.242 2.440 nonbonded pdb=" OG SER A 619 " pdb=" O ASN A 635 " model vdw 2.261 2.440 nonbonded pdb=" O2' A B 175 " pdb=" OP1 A B 176 " model vdw 2.279 2.440 nonbonded pdb=" O2' U B 314 " pdb=" OE2 GLU A 538 " model vdw 2.293 2.440 ... (remaining 96047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 4.620 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.720 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.004 0.049 12968 Z= 0.243 Angle : 0.636 7.614 18644 Z= 0.378 Chirality : 0.039 0.238 2285 Planarity : 0.005 0.042 1542 Dihedral : 16.471 179.261 5533 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.10 (0.28), residues: 924 helix: 1.00 (0.26), residues: 443 sheet: -0.29 (0.51), residues: 93 loop : -1.25 (0.32), residues: 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.101 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.3853 time to fit residues: 25.5463 Evaluate side-chains 32 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 66 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12968 Z= 0.131 Angle : 0.540 8.856 18644 Z= 0.271 Chirality : 0.032 0.177 2285 Planarity : 0.004 0.036 1542 Dihedral : 16.283 179.899 3714 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.44 (0.29), residues: 924 helix: 1.47 (0.26), residues: 453 sheet: -0.10 (0.50), residues: 93 loop : -1.06 (0.33), residues: 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.068 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.2370 time to fit residues: 16.1510 Evaluate side-chains 37 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1192 time to fit residues: 1.7519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12968 Z= 0.161 Angle : 0.514 6.771 18644 Z= 0.259 Chirality : 0.032 0.160 2285 Planarity : 0.004 0.035 1542 Dihedral : 16.157 178.755 3714 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.69 (0.29), residues: 924 helix: 1.69 (0.26), residues: 455 sheet: 0.00 (0.51), residues: 86 loop : -0.95 (0.33), residues: 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 1.055 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.2258 time to fit residues: 13.6721 Evaluate side-chains 33 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1121 time to fit residues: 1.4951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12968 Z= 0.159 Angle : 0.500 8.314 18644 Z= 0.251 Chirality : 0.031 0.158 2285 Planarity : 0.004 0.054 1542 Dihedral : 16.069 178.131 3714 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.29), residues: 924 helix: 1.79 (0.26), residues: 455 sheet: 0.22 (0.53), residues: 86 loop : -0.90 (0.33), residues: 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.138 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.2065 time to fit residues: 14.0165 Evaluate side-chains 35 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1257 time to fit residues: 1.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12968 Z= 0.183 Angle : 0.504 7.864 18644 Z= 0.253 Chirality : 0.032 0.161 2285 Planarity : 0.004 0.034 1542 Dihedral : 16.043 178.079 3714 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 924 helix: 1.85 (0.26), residues: 455 sheet: 0.24 (0.54), residues: 86 loop : -0.87 (0.33), residues: 383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 1.138 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.2058 time to fit residues: 14.1444 Evaluate side-chains 36 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1305 time to fit residues: 2.1405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A 781 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 12968 Z= 0.131 Angle : 0.478 8.099 18644 Z= 0.239 Chirality : 0.030 0.161 2285 Planarity : 0.004 0.034 1542 Dihedral : 15.930 178.002 3714 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.01 (0.29), residues: 924 helix: 1.98 (0.26), residues: 457 sheet: 0.24 (0.54), residues: 86 loop : -0.86 (0.33), residues: 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 1.138 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.1895 time to fit residues: 13.5183 Evaluate side-chains 37 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1192 time to fit residues: 2.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.0000 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 12968 Z= 0.124 Angle : 0.468 7.927 18644 Z= 0.234 Chirality : 0.030 0.160 2285 Planarity : 0.004 0.033 1542 Dihedral : 15.832 177.483 3714 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.17 (0.29), residues: 924 helix: 2.13 (0.26), residues: 457 sheet: 0.26 (0.54), residues: 86 loop : -0.79 (0.33), residues: 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.098 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.1896 time to fit residues: 13.1023 Evaluate side-chains 35 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.0470 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 chunk 10 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 12968 Z= 0.114 Angle : 0.462 8.018 18644 Z= 0.228 Chirality : 0.029 0.161 2285 Planarity : 0.004 0.033 1542 Dihedral : 15.740 177.341 3714 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.30 (0.29), residues: 924 helix: 2.24 (0.26), residues: 457 sheet: 0.32 (0.54), residues: 86 loop : -0.75 (0.33), residues: 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.070 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1875 time to fit residues: 12.8251 Evaluate side-chains 37 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1233 time to fit residues: 1.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.0030 chunk 31 optimal weight: 0.0020 chunk 92 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A1085 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 12968 Z= 0.104 Angle : 0.454 7.883 18644 Z= 0.223 Chirality : 0.029 0.161 2285 Planarity : 0.003 0.031 1542 Dihedral : 15.626 177.204 3714 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.47 (0.30), residues: 924 helix: 2.40 (0.26), residues: 457 sheet: 0.34 (0.53), residues: 86 loop : -0.68 (0.34), residues: 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.165 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.1887 time to fit residues: 15.0506 Evaluate side-chains 39 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.0670 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12968 Z= 0.120 Angle : 0.461 9.002 18644 Z= 0.226 Chirality : 0.029 0.162 2285 Planarity : 0.004 0.032 1542 Dihedral : 15.562 176.898 3714 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.48 (0.29), residues: 924 helix: 2.39 (0.26), residues: 456 sheet: 0.45 (0.54), residues: 86 loop : -0.66 (0.33), residues: 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.105 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1883 time to fit residues: 12.9768 Evaluate side-chains 40 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1285 time to fit residues: 1.5842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 827 GLN A1085 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.146174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089715 restraints weight = 22843.917| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.19 r_work: 0.3050 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12968 Z= 0.208 Angle : 0.497 7.699 18644 Z= 0.247 Chirality : 0.031 0.166 2285 Planarity : 0.004 0.031 1542 Dihedral : 15.606 176.501 3714 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.31 (0.29), residues: 924 helix: 2.26 (0.26), residues: 456 sheet: 0.35 (0.54), residues: 86 loop : -0.76 (0.33), residues: 382 =============================================================================== Job complete usr+sys time: 1902.76 seconds wall clock time: 35 minutes 52.61 seconds (2152.61 seconds total)