Starting phenix.real_space_refine on Sat Mar 16 20:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/03_2024/8atf_15647_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/03_2024/8atf_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_15647/03_2024/8atf_15647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/03_2024/8atf_15647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/03_2024/8atf_15647_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atf_15647/03_2024/8atf_15647_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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. 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-5265/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: 8.85, per 1000 atoms: 0.56 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: 7.08 Conformation dependent library (CDL) restraints added in 1.6 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: 8.78 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: 7.96 Time building geometry restraints manager: 7.64 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: 8034 35.73 - 71.46: 1208 71.46 - 107.18: 22 107.18 - 142.91: 1 142.91 - 178.64: 1 Dihedral angle restraints: 9266 sinusoidal: 5712 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 9263 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 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: 1.360 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: 0.020 Extract box with map and model: 5.200 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 51.810 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 25.037 178.640 6966 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 % Allowed : 6.29 % Favored : 91.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.140 0.024 TRP G1053 HIS 0.030 0.006 HIS S 31 PHE 0.077 0.017 PHE G1152 TYR 0.127 0.017 TYR S 50 ARG 0.069 0.006 ARG G1608 *********************** 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 : 1.345 Fit side-chains REVERT: G 978 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7478 (tptt) REVERT: G 1035 ASN cc_start: 0.7945 (t0) cc_final: 0.7641 (t0) REVERT: G 1135 THR cc_start: 0.8591 (t) cc_final: 0.8266 (t) REVERT: G 1205 HIS cc_start: 0.7080 (m170) cc_final: 0.6855 (m170) REVERT: G 1552 SER cc_start: 0.9273 (t) cc_final: 0.8985 (p) REVERT: G 1563 ARG cc_start: 0.7545 (ttt180) cc_final: 0.7277 (ttm-80) REVERT: G 1606 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8351 (tp30) REVERT: G 1647 ASP cc_start: 0.9364 (p0) cc_final: 0.9108 (t70) REVERT: G 1651 ASN cc_start: 0.8925 (t0) cc_final: 0.8563 (t0) REVERT: G 1659 MET cc_start: 0.8556 (ptp) cc_final: 0.8333 (ptt) REVERT: G 1660 ASP cc_start: 0.8356 (m-30) cc_final: 0.7882 (m-30) REVERT: M 52 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7128 (ttm-80) REVERT: M 53 ARG cc_start: 0.7572 (ttt180) cc_final: 0.7255 (ttm170) REVERT: M 56 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6881 (mttt) REVERT: M 63 ARG cc_start: 0.7164 (mmm-85) cc_final: 0.6913 (mmt-90) REVERT: M 129 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8006 (tpt-90) REVERT: O 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.8110 (m-30) REVERT: P 35 GLU cc_start: 0.8343 (pt0) cc_final: 0.7763 (mt-10) REVERT: P 51 ASP cc_start: 0.8291 (m-30) cc_final: 0.7931 (p0) REVERT: Q 90 MET cc_start: 0.8372 (mmp) cc_final: 0.8036 (tpt) REVERT: R 95 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (ttm110) REVERT: S 104 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7936 (mt0) REVERT: S 111 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8546 (mt) outliers start: 19 outliers final: 5 residues processed: 338 average time/residue: 0.4054 time to fit residues: 180.8463 Evaluate side-chains 213 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 111 ILE 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: 1.9990 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: 2.9990 chunk 84 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN G1657 GLN N 25 ASN N 75 HIS ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN P 95 GLN Q 39 HIS 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: 0.7705 moved from start: 0.2897 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= 0.218 Angle : 0.658 6.186 23614 Z= 0.385 Chirality : 0.039 0.151 2665 Planarity : 0.004 0.037 1991 Dihedral : 28.592 172.957 4499 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.95 % Allowed : 11.05 % Favored : 86.00 % 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: 0.54 (0.23), residues: 1193 helix: 0.79 (0.17), residues: 786 sheet: 0.82 (0.62), residues: 68 loop : -0.56 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G1053 HIS 0.004 0.001 HIS T 82 PHE 0.014 0.002 PHE G1164 TYR 0.023 0.002 TYR G1018 ARG 0.005 0.001 ARG G1017 *********************** 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 246 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: G 1143 MET cc_start: 0.7303 (mpp) cc_final: 0.6366 (tpp) REVERT: G 1205 HIS cc_start: 0.7004 (m170) cc_final: 0.6691 (m170) REVERT: G 1209 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8090 (pm20) REVERT: G 1274 PHE cc_start: 0.7431 (m-80) cc_final: 0.7041 (m-80) REVERT: G 1563 ARG cc_start: 0.7330 (ttt180) cc_final: 0.7127 (ttm-80) REVERT: G 1606 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8605 (tp30) REVERT: G 1694 GLU cc_start: 0.7369 (tt0) cc_final: 0.7081 (tp30) REVERT: M 52 ARG cc_start: 0.7616 (mtt-85) cc_final: 0.5266 (ttt90) REVERT: M 63 ARG cc_start: 0.7015 (mmm-85) cc_final: 0.6748 (mmt-90) REVERT: M 115 LYS cc_start: 0.7188 (mtpp) cc_final: 0.6859 (mmtt) REVERT: M 129 ARG cc_start: 0.8363 (ttt180) cc_final: 0.8053 (tpt-90) REVERT: N 52 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8062 (mt-10) REVERT: P 33 ARG cc_start: 0.6475 (ttt-90) cc_final: 0.6231 (ttm170) REVERT: P 35 GLU cc_start: 0.8181 (pt0) cc_final: 0.7888 (mt-10) REVERT: P 51 ASP cc_start: 0.7998 (m-30) cc_final: 0.7490 (p0) REVERT: P 84 ASN cc_start: 0.8103 (m-40) cc_final: 0.7839 (m110) REVERT: Q 90 MET cc_start: 0.8113 (mmp) cc_final: 0.7754 (tpt) REVERT: R 74 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7786 (tp30) REVERT: S 13 LYS cc_start: 0.6395 (tttt) cc_final: 0.6158 (tptp) REVERT: S 104 GLN cc_start: 0.8230 (mm-40) cc_final: 0.8007 (mt0) REVERT: T 71 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7921 (mp0) outliers start: 31 outliers final: 15 residues processed: 238 average time/residue: 0.3647 time to fit residues: 117.2065 Evaluate side-chains 184 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1089 VAL Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 63 ASN Chi-restraints excluded: chain T residue 90 THR 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: 5.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 981 ASN G1263 GLN N 75 HIS P 63 ASN P 84 ASN Q 39 HIS Q 68 GLN S 31 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16588 Z= 0.286 Angle : 0.629 5.891 23614 Z= 0.366 Chirality : 0.039 0.137 2665 Planarity : 0.004 0.038 1991 Dihedral : 28.485 168.932 4489 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.81 % Allowed : 12.57 % Favored : 83.62 % 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: 1.04 (0.24), residues: 1193 helix: 1.25 (0.18), residues: 780 sheet: 0.65 (0.59), residues: 68 loop : -0.48 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G1053 HIS 0.004 0.001 HIS P 109 PHE 0.012 0.002 PHE M 67 TYR 0.018 0.002 TYR O 50 ARG 0.004 0.000 ARG N 35 *********************** 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 226 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: G 1274 PHE cc_start: 0.7768 (m-80) cc_final: 0.7400 (m-80) REVERT: G 1606 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8481 (tp30) REVERT: M 52 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.5330 (ttt90) REVERT: M 63 ARG cc_start: 0.7320 (mmm-85) cc_final: 0.6924 (mmt-90) REVERT: M 115 LYS cc_start: 0.7349 (mtpp) cc_final: 0.7006 (mmtt) REVERT: M 129 ARG cc_start: 0.8212 (ttt180) cc_final: 0.7821 (tpt-90) REVERT: N 52 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8345 (mt-10) REVERT: P 33 ARG cc_start: 0.6605 (ttt-90) cc_final: 0.6211 (ttm170) REVERT: P 35 GLU cc_start: 0.8222 (pt0) cc_final: 0.7770 (mt-10) REVERT: P 51 ASP cc_start: 0.7983 (m-30) cc_final: 0.7515 (p0) REVERT: Q 90 MET cc_start: 0.8125 (mmp) cc_final: 0.7780 (tpt) REVERT: R 80 THR cc_start: 0.8816 (m) cc_final: 0.8404 (p) outliers start: 40 outliers final: 27 residues processed: 213 average time/residue: 0.3490 time to fit residues: 101.9689 Evaluate side-chains 197 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1005 VAL Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 123 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 122 THR 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: 0.9990 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 63 ASN T 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3986 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 : 0.554 6.038 23614 Z= 0.325 Chirality : 0.035 0.132 2665 Planarity : 0.004 0.037 1991 Dihedral : 28.209 168.020 4488 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.05 % Allowed : 14.19 % Favored : 82.76 % 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: 1.53 (0.24), residues: 1193 helix: 1.69 (0.19), residues: 781 sheet: 0.41 (0.59), residues: 68 loop : -0.33 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.002 0.001 HIS N 75 PHE 0.008 0.001 PHE G1164 TYR 0.011 0.001 TYR G1013 ARG 0.005 0.000 ARG G1664 *********************** 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 208 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: G 1107 ASP cc_start: 0.8825 (t0) cc_final: 0.8610 (t0) REVERT: G 1274 PHE cc_start: 0.7587 (m-80) cc_final: 0.7219 (m-80) REVERT: G 1606 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8423 (tp30) REVERT: M 52 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.5354 (ttt90) REVERT: M 61 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8406 (mt) REVERT: M 63 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6863 (mmt180) REVERT: M 129 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7827 (tpt-90) REVERT: N 52 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8368 (mt-10) REVERT: P 33 ARG cc_start: 0.6604 (ttt-90) cc_final: 0.6246 (ttm170) REVERT: P 35 GLU cc_start: 0.8013 (pt0) cc_final: 0.7557 (mt-10) REVERT: P 51 ASP cc_start: 0.7859 (m-30) cc_final: 0.7326 (p0) REVERT: Q 90 MET cc_start: 0.8041 (mmp) cc_final: 0.7655 (tpt) REVERT: R 74 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7849 (tp30) REVERT: R 80 THR cc_start: 0.8747 (m) cc_final: 0.8446 (p) REVERT: S 110 ASN cc_start: 0.8005 (t0) cc_final: 0.7710 (p0) outliers start: 32 outliers final: 23 residues processed: 194 average time/residue: 0.3558 time to fit residues: 94.6796 Evaluate side-chains 192 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1659 MET Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 63 ASN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4100 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= 0.260 Angle : 0.575 5.807 23614 Z= 0.333 Chirality : 0.036 0.132 2665 Planarity : 0.004 0.044 1991 Dihedral : 28.489 167.118 4488 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.00 % Allowed : 14.29 % Favored : 81.71 % 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: 1.40 (0.24), residues: 1193 helix: 1.59 (0.19), residues: 782 sheet: 0.30 (0.60), residues: 68 loop : -0.37 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G1147 HIS 0.003 0.001 HIS P 109 PHE 0.010 0.001 PHE G1164 TYR 0.015 0.001 TYR O 50 ARG 0.008 0.000 ARG G1664 *********************** 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 216 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: G 1606 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8451 (tp30) REVERT: M 52 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.5342 (ttt90) REVERT: M 63 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6855 (mmt-90) REVERT: M 129 ARG cc_start: 0.8252 (ttt180) cc_final: 0.7903 (tpt-90) REVERT: N 52 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8413 (mt-10) REVERT: P 33 ARG cc_start: 0.6650 (ttt-90) cc_final: 0.6275 (ttm170) REVERT: P 35 GLU cc_start: 0.8031 (pt0) cc_final: 0.7591 (mt-10) REVERT: P 51 ASP cc_start: 0.7861 (m-30) cc_final: 0.7390 (p0) REVERT: Q 70 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7569 (tp) REVERT: Q 90 MET cc_start: 0.8098 (mmp) cc_final: 0.7729 (tpt) REVERT: S 110 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7750 (p0) outliers start: 42 outliers final: 32 residues processed: 202 average time/residue: 0.3284 time to fit residues: 93.1994 Evaluate side-chains 202 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1153 ILE Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain G residue 1659 MET Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 118 VAL 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: 5.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN T 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4243 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= 0.242 Angle : 0.558 5.789 23614 Z= 0.324 Chirality : 0.035 0.130 2665 Planarity : 0.004 0.036 1991 Dihedral : 28.375 166.921 4488 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.00 % Allowed : 15.52 % Favored : 80.48 % 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: 1.44 (0.24), residues: 1193 helix: 1.64 (0.19), residues: 781 sheet: 0.05 (0.60), residues: 68 loop : -0.34 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1147 HIS 0.003 0.001 HIS G1080 PHE 0.008 0.001 PHE G1164 TYR 0.014 0.001 TYR O 50 ARG 0.006 0.000 ARG G1664 *********************** 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 213 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: G 1606 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8456 (tp30) REVERT: M 52 ARG cc_start: 0.7543 (mtt-85) cc_final: 0.5306 (ttt90) REVERT: M 63 ARG cc_start: 0.7317 (mmm-85) cc_final: 0.6916 (mmt-90) REVERT: M 129 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7873 (tpt-90) REVERT: N 52 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8399 (mt-10) REVERT: P 33 ARG cc_start: 0.6647 (ttt-90) cc_final: 0.6274 (ttm170) REVERT: P 35 GLU cc_start: 0.8028 (pt0) cc_final: 0.7633 (mt-10) REVERT: P 51 ASP cc_start: 0.7898 (m-30) cc_final: 0.7410 (p0) REVERT: Q 70 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7576 (tp) REVERT: Q 90 MET cc_start: 0.8091 (mmp) cc_final: 0.7707 (tpt) REVERT: S 110 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7747 (p0) outliers start: 42 outliers final: 33 residues processed: 200 average time/residue: 0.3235 time to fit residues: 90.6496 Evaluate side-chains 203 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1041 SER Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1162 ASP Chi-restraints excluded: chain G residue 1166 GLU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1633 LEU Chi-restraints excluded: chain G residue 1659 MET Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain G residue 1691 LEU Chi-restraints excluded: chain G residue 1699 VAL Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 110 ASN Chi-restraints excluded: chain T residue 63 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.0570 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 102 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1130 ASN P 63 ASN P 67 ASN P 84 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16588 Z= 0.149 Angle : 0.516 5.802 23614 Z= 0.303 Chirality : 0.033 0.169 2665 Planarity : 0.003 0.034 1991 Dihedral : 27.902 165.571 4488 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.38 % Allowed : 17.43 % Favored : 80.19 % 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: 1.89 (0.25), residues: 1193 helix: 1.99 (0.19), residues: 778 sheet: -0.08 (0.60), residues: 67 loop : -0.09 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1147 HIS 0.002 0.000 HIS M 113 PHE 0.007 0.001 PHE G1065 TYR 0.009 0.001 TYR T 40 ARG 0.006 0.000 ARG O 71 *********************** 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 208 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.422 Fit side-chains REVERT: G 1606 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8416 (tp30) REVERT: M 52 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.5306 (ttt90) REVERT: M 61 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8419 (mt) REVERT: M 63 ARG cc_start: 0.7324 (mmm-85) cc_final: 0.7061 (mmp80) REVERT: M 129 ARG cc_start: 0.8264 (ttt180) cc_final: 0.7874 (tpt-90) REVERT: N 52 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8358 (mt-10) REVERT: P 33 ARG cc_start: 0.6634 (ttt-90) cc_final: 0.6245 (ttm170) REVERT: P 35 GLU cc_start: 0.7858 (pt0) cc_final: 0.7464 (mt-10) REVERT: P 51 ASP cc_start: 0.7889 (m-30) cc_final: 0.7392 (p0) REVERT: Q 70 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7381 (tp) REVERT: Q 90 MET cc_start: 0.8021 (mmp) cc_final: 0.7587 (tpt) REVERT: S 110 ASN cc_start: 0.8092 (t0) cc_final: 0.7767 (p0) outliers start: 25 outliers final: 11 residues processed: 198 average time/residue: 0.3405 time to fit residues: 93.4919 Evaluate side-chains 182 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 43 VAL 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: 1.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4614 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= 0.177 Angle : 0.528 7.087 23614 Z= 0.307 Chirality : 0.033 0.138 2665 Planarity : 0.003 0.033 1991 Dihedral : 28.153 165.668 4488 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.00 % 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: 1.89 (0.25), residues: 1193 helix: 1.97 (0.19), residues: 782 sheet: -0.01 (0.61), residues: 67 loop : -0.07 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1147 HIS 0.003 0.001 HIS T 109 PHE 0.006 0.001 PHE G1065 TYR 0.009 0.001 TYR T 40 ARG 0.006 0.000 ARG O 71 *********************** 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 199 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: G 1577 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8881 (mm-40) REVERT: G 1606 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8418 (tp30) REVERT: M 52 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.5331 (ttt90) REVERT: M 61 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8485 (mt) REVERT: M 63 ARG cc_start: 0.7337 (mmm-85) cc_final: 0.6926 (mmt-90) REVERT: M 129 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7866 (tpt-90) REVERT: N 52 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8421 (tt0) REVERT: P 33 ARG cc_start: 0.6655 (ttt-90) cc_final: 0.6263 (ttm170) REVERT: P 35 GLU cc_start: 0.7758 (pt0) cc_final: 0.7385 (mt-10) REVERT: P 51 ASP cc_start: 0.7897 (m-30) cc_final: 0.7363 (p0) REVERT: Q 70 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7365 (tp) REVERT: Q 90 MET cc_start: 0.8116 (mmp) cc_final: 0.7713 (tpt) REVERT: S 110 ASN cc_start: 0.8146 (t0) cc_final: 0.7836 (p0) REVERT: T 86 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7451 (mmt-90) outliers start: 25 outliers final: 15 residues processed: 190 average time/residue: 0.3384 time to fit residues: 89.0615 Evaluate side-chains 186 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Chi-restraints excluded: chain T residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4655 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= 0.181 Angle : 0.532 9.297 23614 Z= 0.307 Chirality : 0.033 0.148 2665 Planarity : 0.003 0.033 1991 Dihedral : 28.122 165.355 4488 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.71 % Allowed : 18.10 % Favored : 80.19 % 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: 1.88 (0.25), residues: 1193 helix: 1.94 (0.19), residues: 782 sheet: 0.09 (0.63), residues: 67 loop : -0.07 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G1147 HIS 0.002 0.000 HIS G1161 PHE 0.006 0.001 PHE G1065 TYR 0.011 0.001 TYR G1646 ARG 0.007 0.000 ARG O 71 *********************** 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 193 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: G 1606 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8416 (tp30) REVERT: M 52 ARG cc_start: 0.7559 (mtt-85) cc_final: 0.5332 (ttt90) REVERT: M 61 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8527 (mt) REVERT: M 63 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6907 (mmt180) REVERT: M 129 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7875 (tpt-90) REVERT: N 52 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8432 (tt0) REVERT: P 33 ARG cc_start: 0.6662 (ttt-90) cc_final: 0.6267 (ttm170) REVERT: P 35 GLU cc_start: 0.7769 (pt0) cc_final: 0.7395 (mt-10) REVERT: P 51 ASP cc_start: 0.7898 (m-30) cc_final: 0.7359 (p0) REVERT: Q 70 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7394 (tp) REVERT: Q 90 MET cc_start: 0.8112 (mmp) cc_final: 0.7710 (tpt) REVERT: S 110 ASN cc_start: 0.8154 (t0) cc_final: 0.7847 (p0) outliers start: 18 outliers final: 14 residues processed: 186 average time/residue: 0.3463 time to fit residues: 89.3245 Evaluate side-chains 186 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7674 moved from start: 0.4697 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= 0.165 Angle : 0.527 8.835 23614 Z= 0.304 Chirality : 0.033 0.141 2665 Planarity : 0.003 0.033 1991 Dihedral : 28.095 165.219 4488 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.62 % Allowed : 18.38 % Favored : 80.00 % 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: 1.94 (0.25), residues: 1193 helix: 1.99 (0.19), residues: 781 sheet: 0.15 (0.63), residues: 67 loop : -0.04 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G1147 HIS 0.002 0.000 HIS G1161 PHE 0.006 0.001 PHE G1065 TYR 0.017 0.001 TYR G1646 ARG 0.007 0.000 ARG O 71 ********************** 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 189 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: G 1581 MET cc_start: 0.8135 (tpt) cc_final: 0.7735 (tpt) REVERT: G 1606 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8433 (tp30) REVERT: M 52 ARG cc_start: 0.7550 (mtt-85) cc_final: 0.5326 (ttt90) REVERT: M 63 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.6894 (mmt180) REVERT: M 129 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7867 (tpt-90) REVERT: N 52 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8459 (tt0) REVERT: P 33 ARG cc_start: 0.6662 (ttt-90) cc_final: 0.6181 (ttm170) REVERT: P 51 ASP cc_start: 0.7896 (m-30) cc_final: 0.7380 (p0) REVERT: Q 70 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7384 (tp) REVERT: Q 90 MET cc_start: 0.8101 (mmp) cc_final: 0.7698 (tpt) REVERT: S 110 ASN cc_start: 0.8152 (t0) cc_final: 0.7847 (p0) outliers start: 17 outliers final: 15 residues processed: 183 average time/residue: 0.3381 time to fit residues: 87.0654 Evaluate side-chains 188 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1014 LEU Chi-restraints excluded: chain G residue 1123 LEU Chi-restraints excluded: chain G residue 1218 VAL Chi-restraints excluded: chain G residue 1260 LEU Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 99 LYS 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: 0.4980 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 101 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111719 restraints weight = 23903.681| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.33 r_work: 0.3202 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4717 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= 0.167 Angle : 0.526 8.353 23614 Z= 0.304 Chirality : 0.033 0.134 2665 Planarity : 0.003 0.034 1991 Dihedral : 28.076 165.107 4486 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.52 % Allowed : 18.48 % Favored : 80.00 % 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: 1.96 (0.25), residues: 1193 helix: 2.00 (0.19), residues: 781 sheet: 0.16 (0.63), residues: 67 loop : -0.02 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G1147 HIS 0.002 0.000 HIS G1161 PHE 0.009 0.001 PHE M 78 TYR 0.013 0.001 TYR G1646 ARG 0.007 0.000 ARG O 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.13 seconds wall clock time: 56 minutes 53.39 seconds (3413.39 seconds total)