Starting phenix.real_space_refine on Mon Apr 15 01:20:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/04_2024/8u3b_41856_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/04_2024/8u3b_41856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/04_2024/8u3b_41856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/04_2024/8u3b_41856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/04_2024/8u3b_41856_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3b_41856/04_2024/8u3b_41856_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 Zn 2 6.06 5 P 142 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20427 2.51 5 N 5918 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 859": "OE1" <-> "OE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 942": "OD1" <-> "OD2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C ASP 995": "OD1" <-> "OD2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ASP 1150": "OD1" <-> "OD2" Residue "C PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1194": "OE1" <-> "OE2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1222": "OE1" <-> "OE2" Residue "C TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1279": "OE1" <-> "OE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D GLU 811": "OE1" <-> "OE2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D GLU 866": "OE1" <-> "OE2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D GLU 981": "OE1" <-> "OE2" Residue "D GLU 1015": "OE1" <-> "OE2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1215": "OE1" <-> "OE2" Residue "D TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1281": "OE1" <-> "OE2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 473": "OE1" <-> "OE2" Residue "F ASP 492": "OD1" <-> "OD2" Residue "F GLU 508": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F ASP 521": "OD1" <-> "OD2" Residue "F ASP 533": "OD1" <-> "OD2" Residue "F GLU 538": "OE1" <-> "OE2" Residue "F ASP 566": "OD1" <-> "OD2" Residue "F TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "G GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33286 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2395 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10576 Classifications: {'peptide': 1341} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Chain: "D" Number of atoms: 10443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10443 Classifications: {'peptide': 1344} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1288} Chain breaks: 2 Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 610 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3516 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 3 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 547 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "H" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 547 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "1" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1415 Classifications: {'DNA': 69} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 68} Chain: "2" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1405 Classifications: {'DNA': 69} Link IDs: {'rna3p': 68} Chain: "3" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15182 SG CYS D 70 48.767 128.993 81.345 1.00166.50 S ATOM 15196 SG CYS D 72 50.044 131.107 78.392 1.00175.94 S ATOM 15304 SG CYS D 85 47.532 128.978 77.734 1.00175.67 S ATOM 15328 SG CYS D 88 50.566 127.098 78.460 1.00169.54 S ATOM 21016 SG CYS D 814 25.816 73.390 114.196 1.00 99.14 S ATOM 21581 SG CYS D 888 29.094 75.032 113.221 1.00 89.23 S ATOM 21632 SG CYS D 895 27.446 76.105 116.422 1.00 82.85 S ATOM 21653 SG CYS D 898 28.851 72.888 116.383 1.00 83.62 S Time building chain proxies: 17.81, per 1000 atoms: 0.54 Number of scatterers: 33286 At special positions: 0 Unit cell: (155.819, 214.251, 202.741, 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 2 29.99 S 136 16.00 P 142 15.00 Mg 1 11.99 O 6660 8.00 N 5918 7.00 C 20427 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.26 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 37 sheets defined 40.2% alpha, 10.8% beta 16 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 15.17 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.640A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.136A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 233 removed outlier: 4.841A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.869A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.827A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.856A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.689A pdb=" N ILE C 209 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 292 No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 456 through 481 removed outlier: 3.670A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 496 through 508 Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 608 through 613 removed outlier: 4.031A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 613' Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 657 through 660 removed outlier: 4.342A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 4.193A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 861 through 864 removed outlier: 3.854A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 979 removed outlier: 4.183A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.262A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 997 No H-bonds generated for 'chain 'C' and resid 995 through 997' Processing helix chain 'C' and resid 1006 through 1037 removed outlier: 3.660A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C1020 " --> pdb=" O GLU C1016 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1110 through 1133 Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1178 removed outlier: 4.802A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 3.638A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1333 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 96 through 99 Processing helix chain 'D' and resid 114 through 118 removed outlier: 4.341A pdb=" N LYS D 118 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.514A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 207 removed outlier: 3.747A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 406 through 416 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 4.041A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 456 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.898A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.692A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 803 removed outlier: 3.997A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 839 No H-bonds generated for 'chain 'D' and resid 836 through 839' Processing helix chain 'D' and resid 866 through 875 Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 929 Proline residue: D 926 - end of helix removed outlier: 5.427A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.210A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.665A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.057A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 13 Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 115 through 136 Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 216 through 235 removed outlier: 4.299A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 removed outlier: 3.666A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 293 removed outlier: 3.962A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 351 removed outlier: 4.465A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 382 removed outlier: 4.019A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 394 removed outlier: 3.832A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 427 through 445 removed outlier: 4.341A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 3.697A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 519 through 522 Processing helix chain 'F' and resid 531 through 550 Processing helix chain 'F' and resid 553 through 563 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 584 through 599 Processing helix chain 'F' and resid 607 through 610 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 158 through 168 Processing helix chain 'G' and resid 173 through 180 Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 203 through 212 Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 158 through 168 Processing helix chain 'H' and resid 173 through 180 Processing helix chain 'H' and resid 184 through 197 Processing helix chain 'H' and resid 203 through 213 removed outlier: 3.654A pdb=" N GLU H 213 " --> pdb=" O TRP H 209 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 189 removed outlier: 3.716A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.818A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 15 removed outlier: 3.814A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.626A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.707A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'C' and resid 116 through 123 removed outlier: 3.644A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.660A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 332 through 336 removed outlier: 5.172A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= O, first strand: chain 'C' and resid 589 through 592 Processing sheet with id= P, first strand: chain 'C' and resid 633 through 638 Processing sheet with id= Q, first strand: chain 'C' and resid 748 through 752 removed outlier: 5.938A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.438A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1065 through 1067 Processing sheet with id= T, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.225A pdb=" N ASP C 303 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 755 through 758 removed outlier: 6.184A pdb=" N ILE C 765 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.549A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.886A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= Y, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= Z, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= AA, first strand: chain 'D' and resid 355 through 357 removed outlier: 6.040A pdb=" N ILE D 447 " --> pdb=" O THR D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 547 through 557 Processing sheet with id= AC, first strand: chain 'D' and resid 706 through 708 Processing sheet with id= AD, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= AE, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AF, first strand: chain 'D' and resid 980 through 983 removed outlier: 4.268A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id= AH, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AI, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id= AJ, first strand: chain 'D' and resid 145 through 149 removed outlier: 7.100A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.689A pdb=" N ILE D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1148 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 13.32 Time building geometry restraints manager: 15.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8127 1.33 - 1.45: 6509 1.45 - 1.57: 18909 1.57 - 1.69: 281 1.69 - 1.81: 240 Bond restraints: 34066 Sorted by residual: bond pdb=" C5 GTP 3 1 " pdb=" C6 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 GTP 3 1 " pdb=" C5 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA ASP D 54 " pdb=" C ASP D 54 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" C MET C1180 " pdb=" N PRO C1181 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.11e-02 8.12e+03 6.33e+00 bond pdb=" CA ALA C 795 " pdb=" CB ALA C 795 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.62e-02 3.81e+03 6.10e+00 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 95.20 - 103.44: 668 103.44 - 111.68: 16813 111.68 - 119.92: 14389 119.92 - 128.16: 14387 128.16 - 136.40: 326 Bond angle restraints: 46583 Sorted by residual: angle pdb=" O3' DG 2 34 " pdb=" C3' DG 2 34 " pdb=" C2' DG 2 34 " ideal model delta sigma weight residual 111.50 96.03 15.47 1.50e+00 4.44e-01 1.06e+02 angle pdb=" N ILE C1109 " pdb=" CA ILE C1109 " pdb=" C ILE C1109 " ideal model delta sigma weight residual 112.83 107.31 5.52 9.90e-01 1.02e+00 3.11e+01 angle pdb=" N GLN C1135 " pdb=" CA GLN C1135 " pdb=" CB GLN C1135 " ideal model delta sigma weight residual 114.17 108.15 6.02 1.14e+00 7.69e-01 2.79e+01 angle pdb=" N SER D 353 " pdb=" CA SER D 353 " pdb=" C SER D 353 " ideal model delta sigma weight residual 107.88 115.19 -7.31 1.41e+00 5.03e-01 2.69e+01 angle pdb=" C LYS D 39 " pdb=" N LYS D 40 " pdb=" CA LYS D 40 " ideal model delta sigma weight residual 122.38 107.93 14.45 2.90e+00 1.19e-01 2.48e+01 ... (remaining 46578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 19898 35.63 - 71.25: 721 71.25 - 106.88: 37 106.88 - 142.51: 1 142.51 - 178.14: 4 Dihedral angle restraints: 20661 sinusoidal: 9542 harmonic: 11119 Sorted by residual: dihedral pdb=" CA ASP C 340 " pdb=" C ASP C 340 " pdb=" N LEU C 341 " pdb=" CA LEU C 341 " ideal model delta harmonic sigma weight residual -180.00 -136.61 -43.39 0 5.00e+00 4.00e-02 7.53e+01 dihedral pdb=" CA GLN C1135 " pdb=" C GLN C1135 " pdb=" N GLN C1136 " pdb=" CA GLN C1136 " ideal model delta harmonic sigma weight residual 180.00 136.84 43.16 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" C5' GTP 3 1 " pdb=" O5' GTP 3 1 " pdb=" PA GTP 3 1 " pdb=" O3A GTP 3 1 " ideal model delta sinusoidal sigma weight residual 69.27 -108.87 178.14 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4289 0.067 - 0.133: 936 0.133 - 0.200: 75 0.200 - 0.267: 12 0.267 - 0.333: 2 Chirality restraints: 5314 Sorted by residual: chirality pdb=" C3' DG 2 34 " pdb=" C4' DG 2 34 " pdb=" O3' DG 2 34 " pdb=" C2' DG 2 34 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C3' DT 1 41 " pdb=" C4' DT 1 41 " pdb=" O3' DT 1 41 " pdb=" C2' DT 1 41 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB THR C1184 " pdb=" CA THR C1184 " pdb=" OG1 THR C1184 " pdb=" CG2 THR C1184 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 5311 not shown) Planarity restraints: 5582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 178 " 0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 179 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 166 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO B 167 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C1135 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLN C1135 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN C1135 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C1136 " 0.016 2.00e-02 2.50e+03 ... (remaining 5579 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 256 2.57 - 3.16: 27951 3.16 - 3.74: 49121 3.74 - 4.32: 67833 4.32 - 4.90: 112294 Nonbonded interactions: 257455 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 1.992 2.170 nonbonded pdb=" O3' A 3 3 " pdb="MG MG D1503 " model vdw 2.046 2.170 nonbonded pdb=" NH2 ARG A 265 " pdb=" O ASN A 294 " model vdw 2.122 2.520 nonbonded pdb=" O GLU C 44 " pdb=" NE2 GLN C 46 " model vdw 2.123 2.520 nonbonded pdb=" NH1 ARG H 203 " pdb=" OP2 DA 1 19 " model vdw 2.127 2.520 ... (remaining 257450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 13.160 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 101.670 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.011 0.090 34066 Z= 0.745 Angle : 0.963 15.465 46583 Z= 0.552 Chirality : 0.053 0.333 5314 Planarity : 0.005 0.072 5582 Dihedral : 16.987 178.135 13485 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 3831 helix: 0.42 (0.13), residues: 1568 sheet: -0.79 (0.22), residues: 463 loop : -1.58 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 433 HIS 0.012 0.002 HIS D 469 PHE 0.038 0.003 PHE B 8 TYR 0.029 0.003 TYR C1285 ARG 0.014 0.001 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.7893 (t70) cc_final: 0.7536 (p0) REVERT: C 337 PHE cc_start: 0.8203 (t80) cc_final: 0.7651 (t80) REVERT: C 339 ASN cc_start: 0.7266 (m110) cc_final: 0.7001 (t0) REVERT: C 1135 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7926 (tp-100) REVERT: D 709 ARG cc_start: 0.6863 (pmt-80) cc_final: 0.5814 (pmt-80) REVERT: E 68 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 69 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8333 (tpp80) REVERT: F 242 HIS cc_start: 0.7600 (t-90) cc_final: 0.7224 (t-90) REVERT: F 561 MET cc_start: 0.8613 (tpp) cc_final: 0.8395 (tpp) REVERT: H 188 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7653 (pptt) REVERT: H 194 MET cc_start: 0.9311 (mmt) cc_final: 0.8799 (mmm) REVERT: H 196 LYS cc_start: 0.8761 (mppt) cc_final: 0.8451 (mptt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5035 time to fit residues: 217.3720 Evaluate side-chains 222 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 chunk 165 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 201 optimal weight: 0.0030 chunk 159 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 357 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D1126 GLN F 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34066 Z= 0.178 Angle : 0.595 11.759 46583 Z= 0.316 Chirality : 0.042 0.175 5314 Planarity : 0.004 0.053 5582 Dihedral : 17.177 172.350 5789 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.33 % Allowed : 5.13 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 3831 helix: 1.02 (0.13), residues: 1574 sheet: -0.48 (0.23), residues: 456 loop : -1.23 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.007 0.001 HIS C1116 PHE 0.021 0.001 PHE D 172 TYR 0.022 0.001 TYR C1018 ARG 0.008 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 247 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3652 (mtt) cc_final: 0.2956 (mpp) REVERT: C 160 ASP cc_start: 0.7720 (t70) cc_final: 0.7433 (p0) REVERT: C 239 MET cc_start: 0.6719 (tmm) cc_final: 0.6508 (tmm) REVERT: C 1304 MET cc_start: 0.8849 (tpp) cc_final: 0.8464 (tpp) REVERT: D 1189 MET cc_start: 0.8698 (tmm) cc_final: 0.8448 (tmm) REVERT: E 68 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 69 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8337 (tpp80) REVERT: E 71 GLU cc_start: 0.8289 (tp30) cc_final: 0.8067 (tp30) REVERT: F 242 HIS cc_start: 0.7470 (t-90) cc_final: 0.7072 (t-90) REVERT: F 561 MET cc_start: 0.8688 (tpp) cc_final: 0.8431 (tpp) REVERT: H 188 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7457 (pptt) REVERT: H 194 MET cc_start: 0.9229 (mmt) cc_final: 0.8948 (mmt) outliers start: 11 outliers final: 7 residues processed: 252 average time/residue: 0.4712 time to fit residues: 195.2690 Evaluate side-chains 234 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 872 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 358 optimal weight: 0.8980 chunk 387 optimal weight: 10.0000 chunk 319 optimal weight: 5.9990 chunk 355 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 287 optimal weight: 50.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 66 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN E 31 GLN E 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34066 Z= 0.302 Angle : 0.587 10.750 46583 Z= 0.311 Chirality : 0.042 0.169 5314 Planarity : 0.004 0.046 5582 Dihedral : 17.085 168.288 5789 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 0.97 % Allowed : 7.52 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3831 helix: 1.20 (0.13), residues: 1573 sheet: -0.36 (0.23), residues: 464 loop : -1.19 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.007 0.001 HIS D 430 PHE 0.023 0.001 PHE D 172 TYR 0.017 0.001 TYR C1087 ARG 0.011 0.001 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3536 (mtt) cc_final: 0.2641 (mpp) REVERT: C 239 MET cc_start: 0.6727 (tmm) cc_final: 0.6478 (tmm) REVERT: C 337 PHE cc_start: 0.8510 (t80) cc_final: 0.8242 (t80) REVERT: D 153 ASN cc_start: 0.7746 (m110) cc_final: 0.7442 (t160) REVERT: D 180 MET cc_start: 0.8591 (ttm) cc_final: 0.8340 (ttm) REVERT: D 715 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8547 (mmmt) REVERT: E 68 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 69 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8384 (tpp80) REVERT: F 242 HIS cc_start: 0.7402 (t-90) cc_final: 0.7115 (t70) REVERT: H 188 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7235 (pptt) REVERT: H 194 MET cc_start: 0.9250 (mmt) cc_final: 0.9024 (mmt) outliers start: 32 outliers final: 14 residues processed: 255 average time/residue: 0.4787 time to fit residues: 201.5081 Evaluate side-chains 232 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1313 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 0.9990 chunk 269 optimal weight: 0.0470 chunk 186 optimal weight: 0.0670 chunk 39 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 359 optimal weight: 6.9990 chunk 380 optimal weight: 0.0670 chunk 187 optimal weight: 0.7980 chunk 340 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34066 Z= 0.140 Angle : 0.509 12.083 46583 Z= 0.271 Chirality : 0.039 0.178 5314 Planarity : 0.004 0.047 5582 Dihedral : 16.946 162.254 5789 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 0.85 % Allowed : 9.18 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3831 helix: 1.50 (0.13), residues: 1575 sheet: 0.01 (0.24), residues: 447 loop : -1.06 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1193 HIS 0.014 0.001 HIS F 600 PHE 0.012 0.001 PHE C 405 TYR 0.018 0.001 TYR C1018 ARG 0.007 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 256 time to evaluate : 4.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3406 (mtt) cc_final: 0.2564 (mpp) REVERT: C 239 MET cc_start: 0.6666 (tmm) cc_final: 0.6426 (tmm) REVERT: C 1016 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: D 29 MET cc_start: 0.8263 (tpp) cc_final: 0.7904 (ttp) REVERT: D 321 LYS cc_start: 0.8455 (ptmm) cc_final: 0.8227 (ptmm) REVERT: D 1040 MET cc_start: 0.4429 (tmm) cc_final: 0.4188 (tmm) REVERT: E 68 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8418 (tm-30) REVERT: F 242 HIS cc_start: 0.7201 (t-90) cc_final: 0.6881 (t70) REVERT: F 561 MET cc_start: 0.8695 (tpp) cc_final: 0.8395 (tpp) REVERT: H 188 LYS cc_start: 0.7670 (ttpt) cc_final: 0.6802 (pptt) REVERT: H 193 HIS cc_start: 0.9348 (m170) cc_final: 0.9117 (m170) REVERT: H 194 MET cc_start: 0.9200 (mmt) cc_final: 0.8891 (mmt) outliers start: 28 outliers final: 10 residues processed: 275 average time/residue: 0.4642 time to fit residues: 213.3297 Evaluate side-chains 232 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain E residue 56 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 283 optimal weight: 30.0000 chunk 157 optimal weight: 2.9990 chunk 324 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN C1080 ASN C1111 GLN D 153 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34066 Z= 0.296 Angle : 0.558 10.507 46583 Z= 0.293 Chirality : 0.041 0.164 5314 Planarity : 0.004 0.044 5582 Dihedral : 16.959 159.571 5789 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 1.15 % Allowed : 10.06 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3831 helix: 1.50 (0.13), residues: 1578 sheet: -0.07 (0.23), residues: 476 loop : -1.05 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.007 0.001 HIS B 132 PHE 0.014 0.001 PHE B 8 TYR 0.018 0.001 TYR C1018 ARG 0.005 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3571 (mtt) cc_final: 0.2695 (mpp) REVERT: C 239 MET cc_start: 0.6774 (tmm) cc_final: 0.6486 (tmm) REVERT: C 959 ASP cc_start: 0.8431 (m-30) cc_final: 0.8159 (m-30) REVERT: C 1016 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: C 1212 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8797 (mp) REVERT: E 68 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8312 (tm-30) REVERT: E 69 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8467 (tpp80) REVERT: F 242 HIS cc_start: 0.7181 (t-90) cc_final: 0.6844 (t70) REVERT: F 397 ARG cc_start: 0.7545 (mtt180) cc_final: 0.6904 (mpp80) REVERT: H 188 LYS cc_start: 0.7700 (ttpt) cc_final: 0.6777 (pptt) REVERT: H 194 MET cc_start: 0.9175 (mmt) cc_final: 0.8868 (mmt) outliers start: 38 outliers final: 26 residues processed: 252 average time/residue: 0.4710 time to fit residues: 197.7928 Evaluate side-chains 243 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 470 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 chunk 316 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 0.0040 chunk 200 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34066 Z= 0.153 Angle : 0.514 13.784 46583 Z= 0.270 Chirality : 0.039 0.171 5314 Planarity : 0.004 0.044 5582 Dihedral : 16.835 159.072 5789 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 0.91 % Allowed : 10.90 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3831 helix: 1.60 (0.13), residues: 1585 sheet: 0.08 (0.24), residues: 471 loop : -0.96 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.009 0.001 HIS H 193 PHE 0.011 0.001 PHE C 405 TYR 0.016 0.001 TYR C1018 ARG 0.005 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 234 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6860 (tmm) cc_final: 0.6559 (tmm) REVERT: C 275 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8470 (tmm160) REVERT: C 959 ASP cc_start: 0.8434 (m-30) cc_final: 0.8128 (m-30) REVERT: C 1016 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: D 29 MET cc_start: 0.8285 (tpp) cc_final: 0.7917 (ttp) REVERT: D 1196 LEU cc_start: 0.8955 (tt) cc_final: 0.8549 (mp) REVERT: E 68 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8364 (tm-30) REVERT: E 69 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8426 (tpp80) REVERT: E 73 GLN cc_start: 0.8950 (tt0) cc_final: 0.8477 (pp30) REVERT: F 242 HIS cc_start: 0.7212 (t-90) cc_final: 0.6882 (t70) REVERT: F 397 ARG cc_start: 0.7437 (mtt180) cc_final: 0.6648 (mpp80) REVERT: F 456 MET cc_start: 0.7992 (tpp) cc_final: 0.7717 (mpp) REVERT: F 561 MET cc_start: 0.8650 (tpp) cc_final: 0.8375 (tpp) REVERT: H 188 LYS cc_start: 0.7529 (ttpt) cc_final: 0.6738 (pptt) outliers start: 30 outliers final: 21 residues processed: 256 average time/residue: 0.4595 time to fit residues: 196.4700 Evaluate side-chains 245 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 379 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS E 15 ASN E 62 GLN F 258 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 34066 Z= 0.423 Angle : 0.629 14.840 46583 Z= 0.329 Chirality : 0.043 0.190 5314 Planarity : 0.004 0.050 5582 Dihedral : 16.943 159.940 5789 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.91 % Rotamer: Outliers : 1.33 % Allowed : 11.02 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3831 helix: 1.36 (0.13), residues: 1581 sheet: -0.01 (0.24), residues: 463 loop : -1.03 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 PHE 0.018 0.002 PHE D 437 TYR 0.020 0.002 TYR C1087 ARG 0.006 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 4.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6840 (tmm) cc_final: 0.6541 (tmm) REVERT: C 241 LEU cc_start: 0.8407 (tp) cc_final: 0.8095 (tt) REVERT: C 959 ASP cc_start: 0.8457 (m-30) cc_final: 0.8056 (m-30) REVERT: C 1191 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8472 (mttm) REVERT: C 1212 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8821 (mp) REVERT: C 1230 MET cc_start: 0.8798 (ttt) cc_final: 0.8572 (ttt) REVERT: E 68 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 75 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8737 (tp40) REVERT: F 242 HIS cc_start: 0.7187 (t-90) cc_final: 0.6840 (t70) REVERT: F 397 ARG cc_start: 0.7653 (mtt180) cc_final: 0.6857 (mpp80) REVERT: F 561 MET cc_start: 0.8674 (tpp) cc_final: 0.8367 (tpp) REVERT: H 188 LYS cc_start: 0.7678 (ttpt) cc_final: 0.6901 (pptt) outliers start: 44 outliers final: 33 residues processed: 246 average time/residue: 0.4742 time to fit residues: 193.3879 Evaluate side-chains 247 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1191 LYS Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 298 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34066 Z= 0.203 Angle : 0.539 13.044 46583 Z= 0.282 Chirality : 0.040 0.166 5314 Planarity : 0.004 0.045 5582 Dihedral : 16.838 158.831 5789 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 1.06 % Allowed : 11.63 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3831 helix: 1.54 (0.13), residues: 1575 sheet: 0.16 (0.24), residues: 468 loop : -0.93 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.009 0.001 HIS G 193 PHE 0.013 0.001 PHE C 405 TYR 0.012 0.001 TYR C1018 ARG 0.011 0.000 ARG D 709 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.6850 (tmm) cc_final: 0.6546 (tmm) REVERT: C 241 LEU cc_start: 0.8431 (tp) cc_final: 0.8095 (tt) REVERT: C 272 ARG cc_start: 0.8913 (mmp80) cc_final: 0.8684 (mmp80) REVERT: C 959 ASP cc_start: 0.8447 (m-30) cc_final: 0.8047 (m-30) REVERT: C 1027 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8444 (pttm) REVERT: C 1230 MET cc_start: 0.8823 (ttt) cc_final: 0.8595 (ttt) REVERT: E 68 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8383 (tm-30) REVERT: F 242 HIS cc_start: 0.7143 (t-90) cc_final: 0.6793 (t70) REVERT: F 397 ARG cc_start: 0.7457 (mtt180) cc_final: 0.6647 (mpp80) REVERT: F 561 MET cc_start: 0.8684 (tpp) cc_final: 0.8357 (tpp) REVERT: H 188 LYS cc_start: 0.7690 (ttpt) cc_final: 0.6939 (pptt) outliers start: 35 outliers final: 27 residues processed: 246 average time/residue: 0.4577 time to fit residues: 187.8936 Evaluate side-chains 239 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 353 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 334 optimal weight: 6.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34066 Z= 0.183 Angle : 0.527 13.715 46583 Z= 0.275 Chirality : 0.040 0.162 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.753 156.782 5789 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 1.00 % Allowed : 11.90 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3831 helix: 1.64 (0.13), residues: 1579 sheet: 0.25 (0.24), residues: 461 loop : -0.85 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1193 HIS 0.009 0.001 HIS G 193 PHE 0.012 0.001 PHE C 405 TYR 0.013 0.001 TYR C1018 ARG 0.008 0.000 ARG D 709 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 HIS cc_start: 0.7944 (p90) cc_final: 0.7728 (p90) REVERT: C 239 MET cc_start: 0.6847 (tmm) cc_final: 0.6545 (tmm) REVERT: C 241 LEU cc_start: 0.8452 (tp) cc_final: 0.8101 (tt) REVERT: C 959 ASP cc_start: 0.8450 (m-30) cc_final: 0.8150 (m-30) REVERT: C 1016 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: C 1230 MET cc_start: 0.8821 (ttt) cc_final: 0.8594 (ttt) REVERT: E 68 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 69 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8461 (tpp80) REVERT: F 96 ASP cc_start: 0.8251 (t0) cc_final: 0.7997 (t0) REVERT: F 242 HIS cc_start: 0.7195 (t-90) cc_final: 0.6859 (t70) REVERT: H 188 LYS cc_start: 0.7702 (ttpt) cc_final: 0.6958 (pptt) outliers start: 33 outliers final: 27 residues processed: 254 average time/residue: 0.4628 time to fit residues: 197.5886 Evaluate side-chains 247 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 219 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 0.0570 chunk 260 optimal weight: 4.9990 chunk 392 optimal weight: 10.0000 chunk 361 optimal weight: 0.9990 chunk 312 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34066 Z= 0.207 Angle : 0.543 16.510 46583 Z= 0.281 Chirality : 0.040 0.165 5314 Planarity : 0.004 0.050 5582 Dihedral : 16.724 155.885 5789 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 0.97 % Allowed : 12.08 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3831 helix: 1.65 (0.13), residues: 1578 sheet: 0.31 (0.25), residues: 462 loop : -0.86 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1193 HIS 0.009 0.001 HIS G 193 PHE 0.012 0.001 PHE C 405 TYR 0.012 0.001 TYR C1018 ARG 0.014 0.000 ARG D 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 HIS cc_start: 0.7919 (p90) cc_final: 0.7680 (p90) REVERT: C 239 MET cc_start: 0.6884 (tmm) cc_final: 0.6579 (tmm) REVERT: C 241 LEU cc_start: 0.8453 (tp) cc_final: 0.8098 (tt) REVERT: C 272 ARG cc_start: 0.8811 (mmp80) cc_final: 0.8483 (mmp80) REVERT: C 959 ASP cc_start: 0.8456 (m-30) cc_final: 0.8154 (m-30) REVERT: C 1016 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: C 1230 MET cc_start: 0.8833 (ttt) cc_final: 0.8565 (ttt) REVERT: D 1174 ARG cc_start: 0.7320 (mmm160) cc_final: 0.7092 (mmm160) REVERT: E 68 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8363 (tm-30) REVERT: E 69 ARG cc_start: 0.8683 (tpp80) cc_final: 0.8478 (tpp80) REVERT: E 75 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8691 (tp40) REVERT: F 96 ASP cc_start: 0.8242 (t0) cc_final: 0.8012 (t0) REVERT: F 242 HIS cc_start: 0.7238 (t-90) cc_final: 0.6905 (t70) REVERT: F 561 MET cc_start: 0.8740 (tpp) cc_final: 0.8534 (tpp) REVERT: H 188 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7011 (pptt) outliers start: 32 outliers final: 28 residues processed: 247 average time/residue: 0.4460 time to fit residues: 183.7593 Evaluate side-chains 250 residues out of total 3310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 6.9990 chunk 332 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 0.0370 chunk 313 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 62 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062264 restraints weight = 99843.981| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.69 r_work: 0.2604 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 0.074 34066 Z= 0.378 Angle : 0.614 13.346 46583 Z= 0.320 Chirality : 0.042 0.181 5314 Planarity : 0.004 0.050 5582 Dihedral : 16.825 156.109 5789 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 1.18 % Allowed : 12.20 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3831 helix: 1.43 (0.13), residues: 1576 sheet: 0.11 (0.25), residues: 454 loop : -0.93 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 PHE 0.016 0.001 PHE B 8 TYR 0.017 0.001 TYR C1087 ARG 0.015 0.001 ARG C 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7368.45 seconds wall clock time: 134 minutes 43.39 seconds (8083.39 seconds total)