Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 20:48:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tre_26087/04_2023/7tre_26087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tre_26087/04_2023/7tre_26087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tre_26087/04_2023/7tre_26087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tre_26087/04_2023/7tre_26087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tre_26087/04_2023/7tre_26087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tre_26087/04_2023/7tre_26087.pdb" } resolution = 3.5 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= 0.004 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 40 5.16 5 C 7660 2.51 5 N 2426 2.21 5 O 3061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" 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 ASP 337": "OD1" <-> "OD2" 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 538": "OE1" <-> "OE2" 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 TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 800": "OE1" <-> "OE2" 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 ASP 860": "OD1" <-> "OD2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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" Residue "A GLU 1116": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ASP 236": "OD1" <-> "OD2" 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: 13411 Number of models: 1 Model: "" Number of chains: 4 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': 20, 'rna3p_pur': 86, 'rna3p_pyr': 97} Link IDs: {'rna2p': 34, 'rna3p': 182} 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: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Time building chain proxies: 7.38, per 1000 atoms: 0.55 Number of scatterers: 13411 At special positions: 0 Unit cell: (140.8, 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 40 16.00 P 224 15.00 O 3061 8.00 N 2426 7.00 C 7660 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: 5.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 50.6% alpha, 14.7% beta 61 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 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 95 through 99 removed outlier: 3.542A pdb=" N PHE A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.512A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.812A pdb=" N LEU A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.730A 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 402 removed outlier: 3.943A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.828A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.628A 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: 3.648A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.908A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.849A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.355A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.664A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.836A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 682 through 699 removed outlier: 3.876A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 856 through 860 removed outlier: 4.160A pdb=" N ASP A 860 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 890 removed outlier: 3.605A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.809A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 4.033A 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: 4.094A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.072A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.675A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.638A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.865A pdb=" N LEU C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.507A pdb=" N LYS C 170 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 223 through 226 Processing helix chain 'C' and resid 227 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.728A pdb=" N GLU A 20 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.973A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 20.101A pdb=" N SER A 797 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600 removed outlier: 4.566A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.537A pdb=" N VAL A 904 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP A 712 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 902 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 120 removed outlier: 7.126A pdb=" N LEU C 145 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL C 120 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR C 143 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 316 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 6.31 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: 2319 1.33 - 1.45: 4595 1.45 - 1.57: 6752 1.57 - 1.69: 444 1.69 - 1.81: 51 Bond restraints: 14161 Sorted by residual: bond pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.41e+00 bond pdb=" N HIS A 609 " pdb=" CA HIS A 609 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.84e+00 bond pdb=" N SER A 134 " pdb=" CA SER A 134 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.22e-02 6.72e+03 6.50e+00 bond pdb=" N ARG A 610 " pdb=" CA ARG A 610 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.32e-02 5.74e+03 6.48e+00 bond pdb=" N LEU A 131 " pdb=" CA LEU A 131 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.21e-02 6.83e+03 6.34e+00 ... (remaining 14156 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.94: 1359 105.94 - 113.02: 7929 113.02 - 120.10: 5198 120.10 - 127.18: 5233 127.18 - 134.26: 547 Bond angle restraints: 20266 Sorted by residual: angle pdb=" C4' A B 62 " pdb=" C3' A B 62 " pdb=" O3' A B 62 " ideal model delta sigma weight residual 113.00 107.88 5.12 1.50e+00 4.44e-01 1.17e+01 angle pdb=" O3' A B 55 " pdb=" C3' A B 55 " pdb=" C2' A B 55 " ideal model delta sigma weight residual 113.70 109.21 4.49 1.50e+00 4.44e-01 8.95e+00 angle pdb=" CA VAL A 127 " pdb=" C VAL A 127 " pdb=" O VAL A 127 " ideal model delta sigma weight residual 121.17 118.09 3.08 1.06e+00 8.90e-01 8.46e+00 angle pdb=" O GLY A 135 " pdb=" C GLY A 135 " pdb=" N ALA A 136 " ideal model delta sigma weight residual 122.19 124.95 -2.76 9.70e-01 1.06e+00 8.10e+00 angle pdb=" O3' G B 71 " pdb=" C3' G B 71 " pdb=" C2' G B 71 " ideal model delta sigma weight residual 113.70 117.95 -4.25 1.50e+00 4.44e-01 8.01e+00 ... (remaining 20261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 7695 35.50 - 70.99: 294 70.99 - 106.49: 24 106.49 - 141.98: 5 141.98 - 177.48: 3 Dihedral angle restraints: 8021 sinusoidal: 4867 harmonic: 3154 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 54.52 177.48 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 232.00 59.89 172.11 1 1.70e+01 3.46e-03 6.61e+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 41.00 -169.00 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 8018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2011 0.054 - 0.109: 371 0.109 - 0.163: 62 0.163 - 0.217: 17 0.217 - 0.271: 8 Chirality restraints: 2469 Sorted by residual: chirality pdb=" P G B 63 " pdb=" OP1 G B 63 " pdb=" OP2 G B 63 " pdb=" O5' G B 63 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' A B 62 " pdb=" C4' A B 62 " pdb=" O3' A B 62 " pdb=" C2' A B 62 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' A B 55 " pdb=" C4' A B 55 " pdb=" O3' A B 55 " pdb=" C2' A B 55 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2466 not shown) Planarity restraints: 1759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 216 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 217 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 167 " 0.027 2.00e-02 2.50e+03 1.26e-02 4.35e+00 pdb=" N9 A B 167 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A B 167 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A B 167 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 167 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 167 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A B 167 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A B 167 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 167 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 167 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 167 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 310 " 0.027 2.00e-02 2.50e+03 1.19e-02 4.23e+00 pdb=" N9 G B 310 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 310 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 310 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 310 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 310 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B 310 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 310 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 310 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 310 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G B 310 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 310 " -0.004 2.00e-02 2.50e+03 ... (remaining 1756 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1175 2.73 - 3.27: 12061 3.27 - 3.82: 22665 3.82 - 4.36: 26991 4.36 - 4.90: 41781 Nonbonded interactions: 104673 Sorted by model distance: nonbonded pdb=" O2' A B 175 " pdb=" OP1 A B 176 " model vdw 2.188 2.440 nonbonded pdb=" O LEU A1079 " pdb=" OG1 THR A1083 " model vdw 2.200 2.440 nonbonded pdb=" O2' U B 314 " pdb=" OE2 GLU A 538 " model vdw 2.203 2.440 nonbonded pdb=" O2' A B 48 " pdb=" OP2 A B 49 " model vdw 2.251 2.440 nonbonded pdb=" N1 G B 93 " pdb=" O6 G B 121 " model vdw 2.253 2.520 ... (remaining 104668 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 4.840 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 41.670 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.006 0.066 14161 Z= 0.399 Angle : 0.767 8.664 20266 Z= 0.418 Chirality : 0.048 0.271 2469 Planarity : 0.005 0.054 1759 Dihedral : 16.745 177.475 5977 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.75 (0.25), residues: 1074 helix: 0.82 (0.24), residues: 477 sheet: -1.09 (0.38), residues: 131 loop : -1.73 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.4043 time to fit residues: 96.8903 Evaluate side-chains 83 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 748 GLN A 779 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14161 Z= 0.182 Angle : 0.600 12.285 20266 Z= 0.296 Chirality : 0.036 0.271 2469 Planarity : 0.005 0.050 1759 Dihedral : 15.945 179.970 3878 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.03 (0.26), residues: 1074 helix: 1.46 (0.24), residues: 479 sheet: -0.84 (0.38), residues: 126 loop : -1.37 (0.29), residues: 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.2629 time to fit residues: 38.6613 Evaluate side-chains 82 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1181 time to fit residues: 3.6518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.0470 chunk 36 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 384 GLN ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 14161 Z= 0.236 Angle : 0.575 15.196 20266 Z= 0.287 Chirality : 0.034 0.204 2469 Planarity : 0.005 0.051 1759 Dihedral : 15.801 179.269 3878 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.17 (0.26), residues: 1074 helix: 1.69 (0.24), residues: 480 sheet: -0.73 (0.39), residues: 124 loop : -1.35 (0.29), residues: 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.2555 time to fit residues: 34.1902 Evaluate side-chains 74 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1340 time to fit residues: 2.2246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN A1051 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14161 Z= 0.135 Angle : 0.516 10.800 20266 Z= 0.254 Chirality : 0.032 0.164 2469 Planarity : 0.004 0.044 1759 Dihedral : 15.588 178.443 3878 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.42 (0.26), residues: 1074 helix: 1.87 (0.24), residues: 482 sheet: -0.43 (0.39), residues: 131 loop : -1.27 (0.30), residues: 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.2782 time to fit residues: 34.2021 Evaluate side-chains 77 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1302 time to fit residues: 3.1725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 14161 Z= 0.129 Angle : 0.501 10.940 20266 Z= 0.247 Chirality : 0.031 0.163 2469 Planarity : 0.004 0.044 1759 Dihedral : 15.438 178.079 3878 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 1074 helix: 1.99 (0.25), residues: 484 sheet: -0.28 (0.39), residues: 131 loop : -1.23 (0.29), residues: 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.2345 time to fit residues: 29.1322 Evaluate side-chains 76 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1318 time to fit residues: 2.6537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14161 Z= 0.199 Angle : 0.529 10.707 20266 Z= 0.263 Chirality : 0.033 0.167 2469 Planarity : 0.004 0.042 1759 Dihedral : 15.447 177.565 3878 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1074 helix: 1.87 (0.25), residues: 487 sheet: -0.28 (0.40), residues: 131 loop : -1.12 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 83 average time/residue: 0.2590 time to fit residues: 32.7452 Evaluate side-chains 72 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1251 time to fit residues: 2.5158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 HIS C 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14161 Z= 0.159 Angle : 0.513 12.211 20266 Z= 0.252 Chirality : 0.032 0.205 2469 Planarity : 0.004 0.042 1759 Dihedral : 15.361 177.476 3878 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.63 (0.27), residues: 1074 helix: 1.97 (0.25), residues: 485 sheet: -0.21 (0.41), residues: 129 loop : -1.13 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 1.314 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.2807 time to fit residues: 32.6356 Evaluate side-chains 69 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1255 time to fit residues: 2.0067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 0.0570 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 11 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14161 Z= 0.119 Angle : 0.500 11.125 20266 Z= 0.244 Chirality : 0.031 0.167 2469 Planarity : 0.004 0.042 1759 Dihedral : 15.261 177.747 3878 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.72 (0.27), residues: 1074 helix: 2.06 (0.25), residues: 483 sheet: -0.15 (0.42), residues: 129 loop : -1.09 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 0.2373 time to fit residues: 27.9801 Evaluate side-chains 70 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2273 time to fit residues: 3.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 0.0770 chunk 122 optimal weight: 9.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 14161 Z= 0.129 Angle : 0.486 10.890 20266 Z= 0.240 Chirality : 0.031 0.168 2469 Planarity : 0.004 0.042 1759 Dihedral : 15.194 177.526 3878 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.77 (0.27), residues: 1074 helix: 2.15 (0.25), residues: 483 sheet: -0.12 (0.43), residues: 129 loop : -1.12 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.2343 time to fit residues: 25.8811 Evaluate side-chains 65 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 0.0070 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 79 optimal weight: 0.0010 chunk 62 optimal weight: 0.2980 chunk 81 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 overall best weight: 0.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14161 Z= 0.111 Angle : 0.480 11.223 20266 Z= 0.234 Chirality : 0.030 0.169 2469 Planarity : 0.004 0.043 1759 Dihedral : 15.086 177.825 3878 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.81 (0.27), residues: 1074 helix: 2.24 (0.25), residues: 483 sheet: -0.09 (0.45), residues: 123 loop : -1.17 (0.29), residues: 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.205 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.2850 time to fit residues: 34.3035 Evaluate side-chains 65 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 827 GLN A 925 HIS C 151 HIS C 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.089569 restraints weight = 27674.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.090373 restraints weight = 16637.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.090386 restraints weight = 12894.773| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14161 Z= 0.247 Angle : 0.554 10.928 20266 Z= 0.274 Chirality : 0.033 0.174 2469 Planarity : 0.004 0.040 1759 Dihedral : 15.212 177.540 3878 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.60 (0.26), residues: 1074 helix: 1.89 (0.25), residues: 487 sheet: -0.07 (0.44), residues: 128 loop : -1.13 (0.29), residues: 459 =============================================================================== Job complete usr+sys time: 1992.62 seconds wall clock time: 38 minutes 46.93 seconds (2326.93 seconds total)