Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 12:15:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5c_26346/04_2023/7u5c_26346_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5c_26346/04_2023/7u5c_26346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5c_26346/04_2023/7u5c_26346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5c_26346/04_2023/7u5c_26346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5c_26346/04_2023/7u5c_26346_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5c_26346/04_2023/7u5c_26346_updated.pdb" } resolution = 4.6 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= 0.002 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 4 6.06 5 P 4 5.49 5 S 164 5.16 5 C 19222 2.51 5 N 5167 2.21 5 O 5512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 445": "OD1" <-> "OD2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 937": "OD1" <-> "OD2" Residue "C PHE 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1350": "OE1" <-> "OE2" Residue "C TYR 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 376": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 558": "OE1" <-> "OE2" Residue "E PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 755": "OE1" <-> "OE2" Residue "E PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 844": "OE1" <-> "OE2" Residue "E ASP 873": "OD1" <-> "OD2" Residue "E ASP 893": "OD1" <-> "OD2" Residue "E PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 901": "OE1" <-> "OE2" Residue "E TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 973": "OE1" <-> "OE2" Residue "E TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1000": "OE1" <-> "OE2" Residue "E TYR 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1160": "OE1" <-> "OE2" Residue "E GLU 1183": "OE1" <-> "OE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "G TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 84": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 30077 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3243 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 16, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain: "C" Number of atoms: 8546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8546 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1003} Chain breaks: 4 Chain: "D" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "E" Number of atoms: 8966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8966 Classifications: {'peptide': 1147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 85, 'TRANS': 1057} Chain breaks: 4 Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1282 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1054 SG CYS A 122 147.918 103.766 173.053 1.00164.53 S ATOM 1093 SG CYS A 128 148.383 106.803 170.627 1.00133.60 S ATOM 14497 SG CYS C1353 83.618 48.265 116.130 1.00 51.91 S ATOM 14647 SG CYS C1371 82.179 51.385 118.366 1.00 40.69 S ATOM 14665 SG CYS C1374 85.454 49.975 118.388 1.00 59.31 S ATOM 13939 SG CYS C1283 81.004 70.826 75.241 1.00 29.87 S ATOM 13959 SG CYS C1286 81.758 68.041 73.680 1.00 31.59 S ATOM 14145 SG CYS C1310 84.483 69.766 74.489 1.00 35.59 S ATOM 26489 SG CYS E1050 51.656 60.994 65.433 1.00153.28 S ATOM 26528 SG CYS E1055 51.829 56.837 64.037 1.00155.72 S Time building chain proxies: 15.56, per 1000 atoms: 0.52 Number of scatterers: 30077 At special positions: 0 Unit cell: (182.52, 158.76, 198.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Fe 4 26.01 S 164 16.00 P 4 15.00 O 5512 8.00 N 5167 7.00 C 19222 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: 12.54 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 424 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 287 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 122 " pdb=" ZN C1501 " pdb="ZN ZN C1501 " - pdb=" SG CYS C1374 " pdb="ZN ZN C1501 " - pdb=" SG CYS C1371 " pdb="ZN ZN C1501 " - pdb=" SG CYS C1353 " pdb=" ZN C1502 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1286 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1283 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1310 " pdb=" ZN E1301 " pdb="ZN ZN E1301 " - pdb=" SG CYS E1050 " pdb="ZN ZN E1301 " - pdb=" SG CYS E1055 " 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 35 sheets defined 30.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.699A pdb=" N ARG A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 34 removed outlier: 6.818A pdb=" N GLY A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 113 through 117 removed outlier: 4.084A pdb=" N ASP A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 149 removed outlier: 4.004A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 210 through 230 removed outlier: 4.208A pdb=" N LYS A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.994A pdb=" N ASP A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLN A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 341' Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 387 through 405 removed outlier: 3.955A pdb=" N VAL A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 68 through 80 removed outlier: 4.037A pdb=" N LEU B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 removed outlier: 5.024A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 132 Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.630A pdb=" N GLU B 163 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN B 164 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 167 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 168 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 211 through 235 removed outlier: 4.141A pdb=" N LEU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 removed outlier: 3.745A pdb=" N SER B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 242' Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.758A pdb=" N ASP B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 305 through 315 removed outlier: 5.097A pdb=" N GLY B 310 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 332 Processing helix chain 'B' and resid 340 through 343 No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 345 through 353 removed outlier: 4.750A pdb=" N PHE B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 385 through 388 No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.874A pdb=" N TYR B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.632A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'C' and resid 410 through 424 removed outlier: 3.670A pdb=" N ALA C 422 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 598 through 605 removed outlier: 4.426A pdb=" N LYS C 604 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 629 Processing helix chain 'C' and resid 639 through 642 No H-bonds generated for 'chain 'C' and resid 639 through 642' Processing helix chain 'C' and resid 644 through 654 Processing helix chain 'C' and resid 659 through 662 Processing helix chain 'C' and resid 682 through 684 No H-bonds generated for 'chain 'C' and resid 682 through 684' Processing helix chain 'C' and resid 696 through 699 Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 725 through 732 removed outlier: 4.215A pdb=" N GLN C 729 " --> pdb=" O GLU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 759 removed outlier: 3.707A pdb=" N MET C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 772 Processing helix chain 'C' and resid 776 through 778 No H-bonds generated for 'chain 'C' and resid 776 through 778' Processing helix chain 'C' and resid 786 through 796 removed outlier: 5.305A pdb=" N LEU C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS C 794 " --> pdb=" O PHE C 790 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 872 Processing helix chain 'C' and resid 876 through 878 No H-bonds generated for 'chain 'C' and resid 876 through 878' Processing helix chain 'C' and resid 911 through 930 removed outlier: 4.008A pdb=" N LYS C 930 " --> pdb=" O LYS C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 961 removed outlier: 4.756A pdb=" N TYR C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY C 958 " --> pdb=" O ASN C 954 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS C 959 " --> pdb=" O SER C 955 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU C 960 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 961 " --> pdb=" O TYR C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 994 removed outlier: 3.581A pdb=" N MET C 994 " --> pdb=" O MET C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1032 removed outlier: 3.733A pdb=" N ASN C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1098 Processing helix chain 'C' and resid 1105 through 1124 removed outlier: 4.552A pdb=" N LEU C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL C1123 " --> pdb=" O ILE C1119 " (cutoff:3.500A) Processing helix chain 'C' and resid 1130 through 1133 Processing helix chain 'C' and resid 1155 through 1164 Processing helix chain 'C' and resid 1195 through 1198 No H-bonds generated for 'chain 'C' and resid 1195 through 1198' Processing helix chain 'C' and resid 1210 through 1213 No H-bonds generated for 'chain 'C' and resid 1210 through 1213' Processing helix chain 'C' and resid 1216 through 1224 removed outlier: 3.813A pdb=" N ILE C1223 " --> pdb=" O VAL C1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 1232 through 1239 Processing helix chain 'C' and resid 1243 through 1248 removed outlier: 3.752A pdb=" N VAL C1248 " --> pdb=" O THR C1244 " (cutoff:3.500A) Processing helix chain 'C' and resid 1270 through 1272 No H-bonds generated for 'chain 'C' and resid 1270 through 1272' Processing helix chain 'C' and resid 1300 through 1302 No H-bonds generated for 'chain 'C' and resid 1300 through 1302' Processing helix chain 'C' and resid 1306 through 1308 No H-bonds generated for 'chain 'C' and resid 1306 through 1308' Processing helix chain 'C' and resid 1319 through 1343 removed outlier: 6.009A pdb=" N VAL C1324 " --> pdb=" O THR C1321 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG C1335 " --> pdb=" O MET C1332 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE C1338 " --> pdb=" O ARG C1335 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR C1342 " --> pdb=" O LYS C1339 " (cutoff:3.500A) Processing helix chain 'C' and resid 1385 through 1398 removed outlier: 3.693A pdb=" N ILE C1398 " --> pdb=" O PHE C1394 " (cutoff:3.500A) Processing helix chain 'C' and resid 1401 through 1406 Processing helix chain 'C' and resid 1411 through 1421 Processing helix chain 'C' and resid 1424 through 1442 Processing helix chain 'C' and resid 1451 through 1453 No H-bonds generated for 'chain 'C' and resid 1451 through 1453' Processing helix chain 'D' and resid 159 through 162 No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 213 through 235 removed outlier: 3.669A pdb=" N ARG D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 399 through 416 removed outlier: 4.691A pdb=" N ILE D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER D 416 " --> pdb=" O GLY D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 476 through 482 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.637A pdb=" N THR D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 528 removed outlier: 5.767A pdb=" N VAL D 527 " --> pdb=" O GLU D 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 16 removed outlier: 4.530A pdb=" N TRP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 26 No H-bonds generated for 'chain 'E' and resid 23 through 26' Processing helix chain 'E' and resid 39 through 53 removed outlier: 4.349A pdb=" N LYS E 47 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 76 removed outlier: 3.890A pdb=" N LEU E 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS E 74 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 346 through 349 Processing helix chain 'E' and resid 390 through 392 No H-bonds generated for 'chain 'E' and resid 390 through 392' Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 450 through 460 removed outlier: 5.044A pdb=" N VAL E 457 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E 460 " --> pdb=" O VAL E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 480 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 503 through 506 No H-bonds generated for 'chain 'E' and resid 503 through 506' Processing helix chain 'E' and resid 508 through 513 Processing helix chain 'E' and resid 524 through 527 No H-bonds generated for 'chain 'E' and resid 524 through 527' Processing helix chain 'E' and resid 552 through 566 Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 585 through 589 Processing helix chain 'E' and resid 787 through 789 No H-bonds generated for 'chain 'E' and resid 787 through 789' Processing helix chain 'E' and resid 802 through 807 Processing helix chain 'E' and resid 883 through 886 No H-bonds generated for 'chain 'E' and resid 883 through 886' Processing helix chain 'E' and resid 913 through 915 No H-bonds generated for 'chain 'E' and resid 913 through 915' Processing helix chain 'E' and resid 1051 through 1053 No H-bonds generated for 'chain 'E' and resid 1051 through 1053' Processing helix chain 'E' and resid 1094 through 1097 No H-bonds generated for 'chain 'E' and resid 1094 through 1097' Processing helix chain 'E' and resid 1101 through 1111 Processing helix chain 'E' and resid 1137 through 1146 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 112 through 120 removed outlier: 4.613A pdb=" N GLN F 117 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'F' and resid 163 through 176 Proline residue: F 171 - end of helix Processing helix chain 'G' and resid 102 through 117 removed outlier: 4.065A pdb=" N GLN G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.540A pdb=" N LEU A 49 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 106 through 110 removed outlier: 3.907A pdb=" N TRP A 157 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 332 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 342 through 344 Processing sheet with id= D, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.769A pdb=" N GLY C 363 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS C 376 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ALA C 518 " --> pdb=" O MET C 379 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 431 through 437 removed outlier: 3.660A pdb=" N LYS C 431 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU C 451 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 539 through 544 removed outlier: 3.559A pdb=" N ALA C 561 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 562 " --> pdb=" O PHE C 583 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 546 through 549 Processing sheet with id= H, first strand: chain 'C' and resid 1039 through 1044 removed outlier: 6.657A pdb=" N LEU C 858 " --> pdb=" O ASP C1041 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL C1043 " --> pdb=" O ILE C 856 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 856 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN C1009 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL C 998 " --> pdb=" O ASN C1009 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 1069 through 1075 removed outlier: 7.413A pdb=" N ALA C1056 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C1049 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU C1058 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU C1047 " --> pdb=" O LEU C1058 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 1135 through 1137 Processing sheet with id= K, first strand: chain 'C' and resid 1280 through 1282 Processing sheet with id= L, first strand: chain 'C' and resid 1346 through 1348 Processing sheet with id= M, first strand: chain 'D' and resid 193 through 195 removed outlier: 7.092A pdb=" N VAL D 537 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR D 472 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 539 " --> pdb=" O THR D 472 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 555 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 540 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 557 " --> pdb=" O ILE D 540 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 283 through 285 removed outlier: 3.766A pdb=" N VAL D 251 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE D 307 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA D 316 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 419 through 423 removed outlier: 3.790A pdb=" N VAL D 423 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL D 374 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 343 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE D 571 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 592 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG D 597 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 170 " --> pdb=" O ARG D 597 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 156 through 160 Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 166 Processing sheet with id= R, first strand: chain 'E' and resid 308 through 310 removed outlier: 3.746A pdb=" N ALA E 280 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER E 248 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU E 233 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE E 246 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 350 through 352 Processing sheet with id= T, first strand: chain 'E' and resid 358 through 361 Processing sheet with id= U, first strand: chain 'E' and resid 407 through 409 Processing sheet with id= V, first strand: chain 'E' and resid 592 through 597 Processing sheet with id= W, first strand: chain 'E' and resid 628 through 630 removed outlier: 3.568A pdb=" N CYS E 650 " --> pdb=" O LEU E 612 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 858 through 862 removed outlier: 6.395A pdb=" N LEU E 766 " --> pdb=" O CYS E 736 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS E 738 " --> pdb=" O TYR E 764 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR E 764 " --> pdb=" O LYS E 738 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 742 through 745 Processing sheet with id= Z, first strand: chain 'E' and resid 934 through 936 removed outlier: 3.596A pdb=" N GLU E 901 " --> pdb=" O ALA E 934 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 899 " --> pdb=" O GLU E 936 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N HIS E 968 " --> pdb=" O VAL E 994 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL E 994 " --> pdb=" O HIS E 968 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER E 970 " --> pdb=" O VAL E 992 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL E 992 " --> pdb=" O SER E 970 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 905 through 907 Processing sheet with id= AB, first strand: chain 'E' and resid 973 through 976 Processing sheet with id= AC, first strand: chain 'E' and resid 1196 through 1198 removed outlier: 6.539A pdb=" N LEU E1076 " --> pdb=" O VAL E1032 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL E1034 " --> pdb=" O ARG E1074 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG E1074 " --> pdb=" O VAL E1034 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 1116 through 1120 Processing sheet with id= AE, first strand: chain 'E' and resid 362 through 365 removed outlier: 6.458A pdb=" N GLU E 374 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 58 through 62 removed outlier: 4.191A pdb=" N ARG F 133 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR F 153 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER F 137 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA F 149 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ARG F 139 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE F 147 " --> pdb=" O ARG F 139 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR F 141 " --> pdb=" O ARG F 145 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG F 145 " --> pdb=" O TYR F 141 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 72 through 78 Processing sheet with id= AH, first strand: chain 'G' and resid 25 through 31 Processing sheet with id= AI, first strand: chain 'G' and resid 41 through 46 911 hydrogen bonds defined for protein. 2391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.04 Time building geometry restraints manager: 13.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 12785 1.43 - 1.64: 17773 1.64 - 1.85: 218 1.85 - 2.06: 0 2.06 - 2.27: 12 Bond restraints: 30788 Sorted by residual: bond pdb=" C PRO E 167 " pdb=" N PRO E 168 " ideal model delta sigma weight residual 1.334 1.498 -0.164 2.34e-02 1.83e+03 4.91e+01 bond pdb=" N LEU E 79 " pdb=" CA LEU E 79 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.12e+01 bond pdb=" N LEU E 106 " pdb=" CA LEU E 106 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.16e-02 7.43e+03 9.22e+00 bond pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.16e-02 7.43e+03 8.86e+00 bond pdb=" C GLY E 100 " pdb=" N PRO E 101 " ideal model delta sigma weight residual 1.333 1.353 -0.020 7.80e-03 1.64e+04 6.77e+00 ... (remaining 30783 not shown) Histogram of bond angle deviations from ideal: 73.66 - 85.98: 12 85.98 - 98.30: 0 98.30 - 110.62: 9565 110.62 - 122.94: 29558 122.94 - 135.26: 2603 Bond angle restraints: 41738 Sorted by residual: angle pdb=" C PRO E 167 " pdb=" N PRO E 168 " pdb=" CA PRO E 168 " ideal model delta sigma weight residual 119.84 135.26 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" N LEU B 250 " pdb=" CA LEU B 250 " pdb=" C LEU B 250 " ideal model delta sigma weight residual 111.36 105.49 5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N ILE B 370 " pdb=" CA ILE B 370 " pdb=" C ILE B 370 " ideal model delta sigma weight residual 112.29 107.23 5.06 9.40e-01 1.13e+00 2.90e+01 angle pdb=" N PRO E 167 " pdb=" CA PRO E 167 " pdb=" C PRO E 167 " ideal model delta sigma weight residual 110.70 104.63 6.07 1.22e+00 6.72e-01 2.47e+01 angle pdb=" N TYR E 92 " pdb=" CA TYR E 92 " pdb=" C TYR E 92 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.21e+01 ... (remaining 41733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 16419 17.53 - 35.06: 1891 35.06 - 52.59: 299 52.59 - 70.12: 54 70.12 - 87.65: 33 Dihedral angle restraints: 18696 sinusoidal: 7744 harmonic: 10952 Sorted by residual: dihedral pdb=" CA VAL D 286 " pdb=" C VAL D 286 " pdb=" N ASP D 287 " pdb=" CA ASP D 287 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA B 191 " pdb=" C ALA B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU E 149 " pdb=" C LEU E 149 " pdb=" N ASP E 150 " pdb=" CA ASP E 150 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 18693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3753 0.062 - 0.123: 794 0.123 - 0.185: 78 0.185 - 0.247: 3 0.247 - 0.308: 2 Chirality restraints: 4630 Sorted by residual: chirality pdb=" CA PRO E 167 " pdb=" N PRO E 167 " pdb=" C PRO E 167 " pdb=" CB PRO E 167 " both_signs ideal model delta sigma weight residual False 2.72 3.03 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LEU B 250 " pdb=" N LEU B 250 " pdb=" C LEU B 250 " pdb=" CB LEU B 250 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ARG E 396 " pdb=" N ARG E 396 " pdb=" C ARG E 396 " pdb=" CB ARG E 396 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4627 not shown) Planarity restraints: 5341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 78 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG E 78 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG E 78 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU E 79 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 423 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO D 424 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 424 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 424 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 432 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO D 433 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 433 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 433 " -0.038 5.00e-02 4.00e+02 ... (remaining 5338 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 479 2.53 - 3.12: 25931 3.12 - 3.71: 48061 3.71 - 4.31: 64130 4.31 - 4.90: 98326 Nonbonded interactions: 236927 Sorted by model distance: nonbonded pdb=" O SER E1048 " pdb="ZN ZN E1301 " model vdw 1.932 2.230 nonbonded pdb=" O ILE E1049 " pdb="ZN ZN E1301 " model vdw 2.010 2.230 nonbonded pdb=" N CYS C1374 " pdb="ZN ZN C1501 " model vdw 2.015 2.310 nonbonded pdb=" CD2 LEU E 142 " pdb=" OH TYR E 165 " model vdw 2.021 3.460 nonbonded pdb=" SG CYS E 81 " pdb=" CZ3 TRP E 163 " model vdw 2.048 3.700 ... (remaining 236922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.030 Extract box with map and model: 8.860 Check model and map are aligned: 0.560 Set scattering table: 0.290 Process input model: 82.550 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.164 30788 Z= 0.374 Angle : 0.866 15.422 41738 Z= 0.476 Chirality : 0.049 0.308 4630 Planarity : 0.006 0.075 5341 Dihedral : 15.088 87.655 11608 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 28.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.36 % Favored : 83.56 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.50 % 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: -5.85 (0.10), residues: 3704 helix: -3.66 (0.10), residues: 1034 sheet: -2.98 (0.20), residues: 517 loop : -4.47 (0.10), residues: 2153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 356 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 366 average time/residue: 0.4648 time to fit residues: 266.7372 Evaluate side-chains 230 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 3.435 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2485 time to fit residues: 7.6188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 336 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 71 GLN A 230 ASN A 231 GLN B 31 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 267 ASN B 410 GLN B 425 GLN B 445 ASN B 452 GLN C 342 HIS ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 HIS ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS C 714 GLN C 727 ASN C 767 GLN C 788 ASN C 862 ASN C 870 GLN C 932 GLN C 986 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 GLN C1132 GLN C1154 HIS ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1250 HIS C1266 GLN C1290 ASN C1420 GLN D 262 ASN D 369 HIS D 419 HIS ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 217 ASN E 241 GLN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 ASN ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 HIS E 869 GLN E 971 GLN E1038 GLN E1177 GLN ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 112 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 30788 Z= 0.221 Angle : 0.711 9.920 41738 Z= 0.365 Chirality : 0.045 0.248 4630 Planarity : 0.005 0.065 5341 Dihedral : 7.215 56.948 4106 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % 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: -4.54 (0.12), residues: 3704 helix: -2.16 (0.13), residues: 1059 sheet: -2.71 (0.20), residues: 546 loop : -3.72 (0.12), residues: 2099 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 346 time to evaluate : 4.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 351 average time/residue: 0.4376 time to fit residues: 248.8332 Evaluate side-chains 224 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 3.789 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2570 time to fit residues: 6.1849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 chunk 363 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1328 ASN D 248 GLN D 262 ASN D 369 HIS ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1020 GLN G 66 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 30788 Z= 0.242 Angle : 0.695 9.775 41738 Z= 0.355 Chirality : 0.045 0.182 4630 Planarity : 0.005 0.061 5341 Dihedral : 7.000 53.169 4106 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.12), residues: 3704 helix: -1.49 (0.14), residues: 1057 sheet: -2.50 (0.20), residues: 567 loop : -3.38 (0.12), residues: 2080 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 312 average time/residue: 0.4214 time to fit residues: 214.2774 Evaluate side-chains 216 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 3.650 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2809 time to fit residues: 5.5118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 357 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 203 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 466 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS ** C 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1067 ASN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 GLN C1412 HIS D 262 ASN D 404 GLN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 30788 Z= 0.390 Angle : 0.813 11.086 41738 Z= 0.412 Chirality : 0.048 0.267 4630 Planarity : 0.006 0.066 5341 Dihedral : 7.354 52.622 4106 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.98 % Favored : 85.02 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.12), residues: 3704 helix: -1.61 (0.14), residues: 1074 sheet: -2.40 (0.20), residues: 558 loop : -3.39 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 280 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 281 average time/residue: 0.4533 time to fit residues: 211.1758 Evaluate side-chains 205 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 3.597 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2537 time to fit residues: 5.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 8.9990 chunk 203 optimal weight: 0.0270 chunk 5 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 305 optimal weight: 50.0000 chunk 247 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 873 ASN C 986 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 GLN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1112 GLN E1177 GLN ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN G 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 30788 Z= 0.335 Angle : 0.769 15.169 41738 Z= 0.390 Chirality : 0.047 0.168 4630 Planarity : 0.006 0.060 5341 Dihedral : 7.225 51.470 4106 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.36 % Favored : 86.64 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.13), residues: 3704 helix: -1.42 (0.15), residues: 1062 sheet: -2.28 (0.20), residues: 575 loop : -3.25 (0.13), residues: 2067 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.4369 time to fit residues: 218.5507 Evaluate side-chains 204 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 3.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 357 optimal weight: 1.9990 chunk 297 optimal weight: 40.0000 chunk 165 optimal weight: 0.0270 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS C 986 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1215 GLN ** C1328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 HIS ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30788 Z= 0.211 Angle : 0.691 11.540 41738 Z= 0.350 Chirality : 0.045 0.175 4630 Planarity : 0.005 0.060 5341 Dihedral : 6.843 52.006 4106 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.39 % Favored : 88.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.13), residues: 3704 helix: -1.03 (0.15), residues: 1070 sheet: -2.14 (0.21), residues: 580 loop : -2.99 (0.13), residues: 2054 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.4034 time to fit residues: 210.0927 Evaluate side-chains 223 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 301 optimal weight: 0.0770 chunk 199 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 ASN C 986 HIS C1023 ASN C1030 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1185 ASN C1252 HIS ** C1328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30788 Z= 0.183 Angle : 0.669 12.758 41738 Z= 0.335 Chirality : 0.044 0.165 4630 Planarity : 0.005 0.056 5341 Dihedral : 6.458 50.917 4106 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.13), residues: 3704 helix: -0.65 (0.16), residues: 1050 sheet: -1.94 (0.21), residues: 554 loop : -2.75 (0.13), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.4118 time to fit residues: 223.5579 Evaluate side-chains 225 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 986 HIS ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 GLN ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30788 Z= 0.214 Angle : 0.667 11.004 41738 Z= 0.336 Chirality : 0.044 0.165 4630 Planarity : 0.005 0.055 5341 Dihedral : 6.392 50.943 4106 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.14), residues: 3704 helix: -0.55 (0.16), residues: 1046 sheet: -1.81 (0.22), residues: 553 loop : -2.69 (0.13), residues: 2105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 4.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.4241 time to fit residues: 215.5651 Evaluate side-chains 225 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.604 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 311 optimal weight: 0.0470 chunk 332 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 260 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 331 optimal weight: 5.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30788 Z= 0.194 Angle : 0.659 11.488 41738 Z= 0.329 Chirality : 0.044 0.203 4630 Planarity : 0.005 0.055 5341 Dihedral : 6.272 50.940 4106 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 3704 helix: -0.47 (0.16), residues: 1047 sheet: -1.77 (0.21), residues: 582 loop : -2.57 (0.14), residues: 2075 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.4381 time to fit residues: 224.5158 Evaluate side-chains 232 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 368 optimal weight: 20.0000 chunk 339 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 452 GLN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS C1328 ASN ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 30788 Z= 0.197 Angle : 0.669 15.469 41738 Z= 0.332 Chirality : 0.044 0.181 4630 Planarity : 0.005 0.055 5341 Dihedral : 6.206 51.013 4106 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.14), residues: 3704 helix: -0.40 (0.16), residues: 1043 sheet: -1.72 (0.21), residues: 591 loop : -2.52 (0.14), residues: 2070 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.4225 time to fit residues: 217.4303 Evaluate side-chains 227 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 3.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 270 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 301 optimal weight: 0.0070 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 HIS ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.108162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086142 restraints weight = 123843.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084258 restraints weight = 111108.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084646 restraints weight = 105335.570| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 30788 Z= 0.165 Angle : 0.640 9.880 41738 Z= 0.317 Chirality : 0.043 0.155 4630 Planarity : 0.005 0.098 5341 Dihedral : 6.003 51.342 4106 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 3704 helix: -0.29 (0.16), residues: 1047 sheet: -1.54 (0.21), residues: 579 loop : -2.43 (0.14), residues: 2078 =============================================================================== Job complete usr+sys time: 5216.36 seconds wall clock time: 102 minutes 53.27 seconds (6173.27 seconds total)