Starting phenix.real_space_refine (version: dev) on Tue Feb 21 20:54:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/02_2023/8atf_15647_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/02_2023/8atf_15647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/02_2023/8atf_15647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/02_2023/8atf_15647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/02_2023/8atf_15647_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/02_2023/8atf_15647_updated.pdb" } resolution = 3.45 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 Process input model Symmetric amino acids flipped Residue "G ARG 1017": "NH1" <-> "NH2" Residue "G ARG 1059": "NH1" <-> "NH2" Residue "G ARG 1063": "NH1" <-> "NH2" Residue "G PHE 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1068": "NH1" <-> "NH2" Residue "G ARG 1119": "NH1" <-> "NH2" Residue "G ARG 1129": "NH1" <-> "NH2" Residue "G ARG 1131": "NH1" <-> "NH2" Residue "G ARG 1189": "NH1" <-> "NH2" Residue "G ARG 1200": "NH1" <-> "NH2" Residue "G ARG 1201": "NH1" <-> "NH2" Residue "G ARG 1225": "NH1" <-> "NH2" Residue "G ARG 1227": "NH1" <-> "NH2" Residue "G ARG 1234": "NH1" <-> "NH2" Residue "G ARG 1265": "NH1" <-> "NH2" Residue "G ARG 1276": "NH1" <-> "NH2" Residue "G ARG 1547": "NH1" <-> "NH2" Residue "G ARG 1563": "NH1" <-> "NH2" Residue "G ARG 1571": "NH1" <-> "NH2" Residue "G PHE 1576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1580": "NH1" <-> "NH2" Residue "G TYR 1588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1592": "NH1" <-> "NH2" Residue "G ARG 1598": "NH1" <-> "NH2" Residue "G ARG 1608": "NH1" <-> "NH2" Residue "G ARG 1609": "NH1" <-> "NH2" Residue "G ARG 1618": "NH1" <-> "NH2" Residue "G ARG 1629": "NH1" <-> "NH2" Residue "G ARG 1661": "NH1" <-> "NH2" Residue "G ARG 1664": "NH1" <-> "NH2" Residue "G ARG 1675": "NH1" <-> "NH2" Residue "G ARG 1679": "NH1" <-> "NH2" Residue "G ARG 1685": "NH1" <-> "NH2" Residue "G ARG 1687": "NH1" <-> "NH2" Residue "G ARG 1689": "NH1" <-> "NH2" Residue "G ARG 1698": "NH1" <-> "NH2" Residue "H ARG 390": "NH1" <-> "NH2" Residue "H ARG 391": "NH1" <-> "NH2" Residue "H ARG 392": "NH1" <-> "NH2" Residue "H ARG 393": "NH1" <-> "NH2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "M ARG 42": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 83": "NH1" <-> "NH2" Residue "M ARG 116": "NH1" <-> "NH2" Residue "M ARG 128": "NH1" <-> "NH2" Residue "M ARG 129": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "N ARG 35": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 39": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N ARG 92": "NH1" <-> "NH2" Residue "N ARG 95": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 29": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 72": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P ARG 86": "NH1" <-> "NH2" Residue "P ARG 92": "NH1" <-> "NH2" Residue "P ARG 99": "NH1" <-> "NH2" Residue "P TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 49": "NH1" <-> "NH2" Residue "Q ARG 52": "NH1" <-> "NH2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 116": "NH1" <-> "NH2" Residue "Q ARG 128": "NH1" <-> "NH2" Residue "Q ARG 129": "NH1" <-> "NH2" Residue "Q ARG 131": "NH1" <-> "NH2" Residue "R ARG 35": "NH1" <-> "NH2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "R ARG 39": "NH1" <-> "NH2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 17": "NH1" <-> "NH2" Residue "S ARG 20": "NH1" <-> "NH2" Residue "S ARG 29": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 35": "NH1" <-> "NH2" Residue "S ARG 42": "NH1" <-> "NH2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "S ARG 77": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "T TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 72": "NH1" <-> "NH2" Residue "T ARG 79": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15719 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3661 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 428} Chain breaks: 3 Chain: "H" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "K" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "L" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "M" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "N" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "O" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "P" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "R" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "T" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.27, per 1000 atoms: 0.59 Number of scatterers: 15719 At special positions: 0 Unit cell: (120.726, 140.847, 145.083, 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 35 16.00 P 288 15.00 O 3474 8.00 N 2908 7.00 C 9014 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: 7.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 2 sheets defined 60.1% alpha, 3.8% beta 141 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'G' and resid 974 through 989 Processing helix chain 'G' and resid 1003 through 1017 removed outlier: 3.634A pdb=" N MET G1011 " --> pdb=" O SER G1007 " (cutoff:3.500A) Processing helix chain 'G' and resid 1030 through 1043 removed outlier: 4.630A pdb=" N HIS G1034 " --> pdb=" O SER G1031 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G1040 " --> pdb=" O GLN G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1056 through 1065 removed outlier: 4.015A pdb=" N VAL G1061 " --> pdb=" O ALA G1057 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE G1065 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1086 through 1091 Processing helix chain 'G' and resid 1093 through 1098 removed outlier: 4.813A pdb=" N LYS G1098 " --> pdb=" O ALA G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1109 through 1112 Processing helix chain 'G' and resid 1118 through 1125 removed outlier: 4.366A pdb=" N GLY G1125 " --> pdb=" O LYS G1121 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1153 removed outlier: 3.513A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1161 through 1165 Processing helix chain 'G' and resid 1184 through 1193 removed outlier: 3.594A pdb=" N MET G1192 " --> pdb=" O LYS G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1203 through 1205 No H-bonds generated for 'chain 'G' and resid 1203 through 1205' Processing helix chain 'G' and resid 1224 through 1235 Processing helix chain 'G' and resid 1261 through 1269 Processing helix chain 'G' and resid 1271 through 1273 No H-bonds generated for 'chain 'G' and resid 1271 through 1273' Processing helix chain 'G' and resid 1545 through 1550 Processing helix chain 'G' and resid 1553 through 1568 removed outlier: 3.630A pdb=" N GLU G1560 " --> pdb=" O ALA G1556 " (cutoff:3.500A) Processing helix chain 'G' and resid 1579 through 1592 removed outlier: 3.869A pdb=" N GLU G1587 " --> pdb=" O ASP G1583 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR G1588 " --> pdb=" O LEU G1584 " (cutoff:3.500A) Processing helix chain 'G' and resid 1605 through 1617 removed outlier: 4.020A pdb=" N ARG G1609 " --> pdb=" O LEU G1605 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP G1610 " --> pdb=" O GLU G1606 " (cutoff:3.500A) Processing helix chain 'G' and resid 1628 through 1631 No H-bonds generated for 'chain 'G' and resid 1628 through 1631' Processing helix chain 'G' and resid 1652 through 1662 removed outlier: 3.788A pdb=" N ARG G1661 " --> pdb=" O GLN G1657 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA G1662 " --> pdb=" O ALA G1658 " (cutoff:3.500A) Processing helix chain 'G' and resid 1682 through 1701 Processing helix chain 'H' and resid 390 through 415 removed outlier: 3.638A pdb=" N GLU H 397 " --> pdb=" O ARG H 393 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS H 398 " --> pdb=" O ASN H 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 403 " --> pdb=" O ARG H 399 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 412 " --> pdb=" O VAL H 408 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 54 Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.198A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 114 Processing helix chain 'M' and resid 121 through 131 Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 31 through 40 Processing helix chain 'N' and resid 49 through 75 removed outlier: 3.525A pdb=" N GLU N 53 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG N 55 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE N 66 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG N 67 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL N 70 " --> pdb=" O ARG N 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU N 74 " --> pdb=" O THR N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 93 removed outlier: 3.913A pdb=" N GLN N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 21 Processing helix chain 'O' and resid 27 through 36 Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.051A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU O 65 " --> pdb=" O GLU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 91 through 96 Processing helix chain 'O' and resid 113 through 115 No H-bonds generated for 'chain 'O' and resid 113 through 115' Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.518A pdb=" N LYS P 43 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 84 Processing helix chain 'P' and resid 91 through 101 Processing helix chain 'P' and resid 104 through 123 removed outlier: 3.780A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 55 Processing helix chain 'Q' and resid 64 through 77 removed outlier: 4.237A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 113 Processing helix chain 'Q' and resid 121 through 130 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 31 through 41 Processing helix chain 'R' and resid 50 through 75 removed outlier: 3.518A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 92 removed outlier: 3.537A pdb=" N ARG R 92 " --> pdb=" O TYR R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 21 Processing helix chain 'S' and resid 27 through 36 Processing helix chain 'S' and resid 45 through 72 removed outlier: 4.189A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 89 Processing helix chain 'S' and resid 91 through 96 Processing helix chain 'T' and resid 38 through 48 Processing helix chain 'T' and resid 56 through 84 Processing helix chain 'T' and resid 92 through 101 Processing helix chain 'T' and resid 104 through 123 removed outlier: 3.639A pdb=" N HIS T 109 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY T 114 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR T 121 " --> pdb=" O VAL T 118 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 993 through 995 removed outlier: 3.562A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 1214 through 1220 505 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 8.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2342 1.32 - 1.46: 6757 1.46 - 1.60: 6870 1.60 - 1.74: 557 1.74 - 1.88: 62 Bond restraints: 16588 Sorted by residual: bond pdb=" C4 ADP G2000 " pdb=" C5 ADP G2000 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C GLN T 95 " pdb=" O GLN T 95 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.17e-02 7.31e+03 2.22e+01 bond pdb=" C5 ADP G2000 " pdb=" C6 ADP G2000 " ideal model delta sigma weight residual 1.490 1.399 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CA SER M 96 " pdb=" CB SER M 96 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CG ASP G1092 " pdb=" OD2 ASP G1092 " ideal model delta sigma weight residual 1.249 1.322 -0.073 1.90e-02 2.77e+03 1.46e+01 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 88.42 - 97.82: 36 97.82 - 107.23: 2890 107.23 - 116.63: 9829 116.63 - 126.04: 9958 126.04 - 135.44: 901 Bond angle restraints: 23614 Sorted by residual: angle pdb=" O3' DC L -25 " pdb=" P DT L -24 " pdb=" O5' DT L -24 " ideal model delta sigma weight residual 104.00 92.97 11.03 1.50e+00 4.44e-01 5.41e+01 angle pdb=" NE ARG M 52 " pdb=" CZ ARG M 52 " pdb=" NH1 ARG M 52 " ideal model delta sigma weight residual 121.50 114.19 7.31 1.00e+00 1.00e+00 5.34e+01 angle pdb=" NE ARG M 52 " pdb=" CZ ARG M 52 " pdb=" NH2 ARG M 52 " ideal model delta sigma weight residual 119.20 125.74 -6.54 9.00e-01 1.23e+00 5.29e+01 angle pdb=" O3' DA K -5 " pdb=" P DC K -4 " pdb=" O5' DC K -4 " ideal model delta sigma weight residual 104.00 94.08 9.92 1.50e+00 4.44e-01 4.38e+01 angle pdb=" O3' DT L 15 " pdb=" C3' DT L 15 " pdb=" C2' DT L 15 " ideal model delta sigma weight residual 111.50 101.63 9.87 1.50e+00 4.44e-01 4.33e+01 ... (remaining 23609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 7822 35.73 - 71.46: 1172 71.46 - 107.18: 22 107.18 - 142.91: 1 142.91 - 178.64: 1 Dihedral angle restraints: 9018 sinusoidal: 5464 harmonic: 3554 Sorted by residual: dihedral pdb=" CA ARG G1664 " pdb=" C ARG G1664 " pdb=" N LEU G1665 " pdb=" CA LEU G1665 " ideal model delta harmonic sigma weight residual 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA GLU G 998 " pdb=" C GLU G 998 " pdb=" N MET G 999 " pdb=" CA MET G 999 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO P 103 " pdb=" C PRO P 103 " pdb=" N GLY P 104 " pdb=" CA GLY P 104 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 9015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2178 0.130 - 0.259: 385 0.259 - 0.389: 90 0.389 - 0.518: 7 0.518 - 0.648: 5 Chirality restraints: 2665 Sorted by residual: chirality pdb=" P DG L -70 " pdb=" OP1 DG L -70 " pdb=" OP2 DG L -70 " pdb=" O5' DG L -70 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DT K -72 " pdb=" OP1 DT K -72 " pdb=" OP2 DT K -72 " pdb=" O5' DT K -72 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DA L -12 " pdb=" OP1 DA L -12 " pdb=" OP2 DA L -12 " pdb=" O5' DA L -12 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 2662 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 50 " 0.127 2.00e-02 2.50e+03 7.14e-02 1.02e+02 pdb=" CG TYR S 50 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR S 50 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR S 50 " -0.114 2.00e-02 2.50e+03 pdb=" CE1 TYR S 50 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR S 50 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR S 50 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR S 50 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC K 37 " 0.136 2.00e-02 2.50e+03 6.21e-02 8.69e+01 pdb=" N1 DC K 37 " -0.065 2.00e-02 2.50e+03 pdb=" C2 DC K 37 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC K 37 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DC K 37 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DC K 37 " 0.024 2.00e-02 2.50e+03 pdb=" N4 DC K 37 " 0.059 2.00e-02 2.50e+03 pdb=" C5 DC K 37 " -0.035 2.00e-02 2.50e+03 pdb=" C6 DC K 37 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G1053 " -0.059 2.00e-02 2.50e+03 5.66e-02 8.01e+01 pdb=" CG TRP G1053 " 0.140 2.00e-02 2.50e+03 pdb=" CD1 TRP G1053 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP G1053 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP G1053 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TRP G1053 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP G1053 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP G1053 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP G1053 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP G1053 " 0.015 2.00e-02 2.50e+03 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 334 2.65 - 3.21: 13022 3.21 - 3.78: 26420 3.78 - 4.34: 37969 4.34 - 4.90: 53400 Nonbonded interactions: 131145 Sorted by model distance: nonbonded pdb=" O HIS R 75 " pdb=" NH2 ARG T 92 " model vdw 2.090 2.520 nonbonded pdb=" OP2 DA K 17 " pdb=" NH2 ARG Q 69 " model vdw 2.201 2.520 nonbonded pdb=" O SER Q 57 " pdb=" NH1 ARG R 40 " model vdw 2.300 2.520 nonbonded pdb=" NH2 ARG S 32 " pdb=" OE1 GLU T 35 " model vdw 2.324 2.520 nonbonded pdb=" O PHE N 100 " pdb=" C GLY N 101 " model vdw 2.344 3.270 ... (remaining 131140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 40 through 134) } ncs_group { reference = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = (chain 'P' and resid 34 through 124) selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 35 5.16 5 C 9014 2.51 5 N 2908 2.21 5 O 3474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.940 Check model and map are aligned: 0.260 Process input model: 50.420 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.013 0.105 16588 Z= 0.745 Angle : 1.988 19.581 23614 Z= 1.223 Chirality : 0.111 0.648 2665 Planarity : 0.026 0.255 1991 Dihedral : 24.983 178.640 6718 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.10 % Favored : 96.23 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1193 helix: -1.38 (0.15), residues: 777 sheet: 0.55 (0.64), residues: 68 loop : -1.34 (0.28), residues: 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 324 time to evaluate : 1.447 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 338 average time/residue: 0.4212 time to fit residues: 188.9159 Evaluate side-chains 205 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1453 time to fit residues: 3.2271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN N 25 ASN N 75 HIS ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN P 95 GLN Q 39 HIS Q 68 GLN R 25 ASN R 75 HIS T 63 ASN T 82 HIS T 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 16588 Z= 0.221 Angle : 0.654 6.080 23614 Z= 0.384 Chirality : 0.039 0.139 2665 Planarity : 0.004 0.040 1991 Dihedral : 29.011 173.082 4237 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.58 (0.23), residues: 1193 helix: 0.82 (0.18), residues: 785 sheet: 0.85 (0.63), residues: 68 loop : -0.56 (0.31), residues: 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.409 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 229 average time/residue: 0.3648 time to fit residues: 114.0463 Evaluate side-chains 178 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1742 time to fit residues: 5.2272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 142 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 981 ASN P 63 ASN Q 39 HIS S 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16588 Z= 0.190 Angle : 0.576 5.864 23614 Z= 0.340 Chirality : 0.036 0.127 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.510 168.703 4237 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.46 (0.24), residues: 1193 helix: 1.53 (0.18), residues: 789 sheet: 0.85 (0.59), residues: 68 loop : -0.23 (0.33), residues: 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.529 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 195 average time/residue: 0.3689 time to fit residues: 98.0528 Evaluate side-chains 177 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1323 time to fit residues: 4.2730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 132 optimal weight: 0.0270 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16588 Z= 0.157 Angle : 0.530 6.362 23614 Z= 0.313 Chirality : 0.033 0.137 2665 Planarity : 0.003 0.049 1991 Dihedral : 28.431 167.167 4237 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.83 (0.24), residues: 1193 helix: 1.88 (0.19), residues: 785 sheet: 0.65 (0.59), residues: 68 loop : -0.15 (0.33), residues: 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.553 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 185 average time/residue: 0.3600 time to fit residues: 91.9824 Evaluate side-chains 175 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3202 time to fit residues: 5.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1140 GLN H 415 GLN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 16588 Z= 0.285 Angle : 0.582 5.919 23614 Z= 0.336 Chirality : 0.036 0.133 2665 Planarity : 0.004 0.034 1991 Dihedral : 28.859 167.163 4237 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.52 (0.24), residues: 1193 helix: 1.66 (0.19), residues: 782 sheet: 0.44 (0.60), residues: 68 loop : -0.32 (0.33), residues: 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.455 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 183 average time/residue: 0.3387 time to fit residues: 86.7140 Evaluate side-chains 174 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1406 time to fit residues: 3.5289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16588 Z= 0.213 Angle : 0.545 7.325 23614 Z= 0.316 Chirality : 0.034 0.127 2665 Planarity : 0.004 0.034 1991 Dihedral : 28.704 166.418 4237 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.58 (0.24), residues: 1193 helix: 1.74 (0.19), residues: 782 sheet: 0.22 (0.60), residues: 68 loop : -0.33 (0.33), residues: 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.441 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 176 average time/residue: 0.3541 time to fit residues: 86.8330 Evaluate side-chains 170 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1241 time to fit residues: 2.4903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16588 Z= 0.163 Angle : 0.520 7.326 23614 Z= 0.303 Chirality : 0.033 0.128 2665 Planarity : 0.003 0.033 1991 Dihedral : 28.511 165.669 4237 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.83 (0.25), residues: 1193 helix: 1.95 (0.19), residues: 781 sheet: 0.16 (0.60), residues: 68 loop : -0.20 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.691 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 175 average time/residue: 0.3562 time to fit residues: 86.2613 Evaluate side-chains 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1529 time to fit residues: 2.8819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16588 Z= 0.214 Angle : 0.547 6.923 23614 Z= 0.313 Chirality : 0.034 0.127 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.749 165.559 4237 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.74 (0.25), residues: 1193 helix: 1.85 (0.19), residues: 781 sheet: 0.12 (0.62), residues: 68 loop : -0.19 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.499 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 0.3552 time to fit residues: 87.0072 Evaluate side-chains 171 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1395 time to fit residues: 2.0514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16588 Z= 0.180 Angle : 0.535 6.586 23614 Z= 0.308 Chirality : 0.034 0.129 2665 Planarity : 0.003 0.034 1991 Dihedral : 28.647 165.320 4237 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.82 (0.25), residues: 1193 helix: 1.92 (0.19), residues: 782 sheet: 0.05 (0.61), residues: 68 loop : -0.13 (0.34), residues: 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.451 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.3464 time to fit residues: 84.1746 Evaluate side-chains 172 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1474 time to fit residues: 2.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16588 Z= 0.162 Angle : 0.531 8.106 23614 Z= 0.305 Chirality : 0.033 0.130 2665 Planarity : 0.003 0.033 1991 Dihedral : 28.595 165.036 4237 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.92 (0.25), residues: 1193 helix: 2.00 (0.19), residues: 781 sheet: -0.02 (0.61), residues: 68 loop : -0.08 (0.34), residues: 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.501 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 172 average time/residue: 0.3563 time to fit residues: 85.8381 Evaluate side-chains 171 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1365 time to fit residues: 2.3178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 113 HIS ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110969 restraints weight = 23768.161| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.33 r_work: 0.3193 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16588 Z= 0.187 Angle : 0.537 8.025 23614 Z= 0.307 Chirality : 0.034 0.136 2665 Planarity : 0.004 0.039 1991 Dihedral : 28.631 164.948 4237 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.87 (0.25), residues: 1193 helix: 1.96 (0.19), residues: 782 sheet: -0.11 (0.60), residues: 68 loop : -0.09 (0.34), residues: 343 =============================================================================== Job complete usr+sys time: 3096.98 seconds wall clock time: 56 minutes 28.13 seconds (3388.13 seconds total)