Starting phenix.real_space_refine (version: dev) on Fri Apr 8 05:10:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkd_23892/04_2022/7mkd_23892_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.111 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G GLU 67": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 393": "OD1" <-> "OD2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I ASP 624": "OD1" <-> "OD2" Residue "I GLU 625": "OE1" <-> "OE2" Residue "I PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 654": "OD1" <-> "OD2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I ARG 1147": "NH1" <-> "NH2" Residue "I GLU 1192": "OE1" <-> "OE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1289": "OE1" <-> "OE2" Residue "I ASP 1296": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 925": "OE1" <-> "OE2" Residue "J GLU 1236": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "L TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 247": "OE1" <-> "OE2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 310": "OE1" <-> "OE2" Residue "L GLU 336": "OE1" <-> "OE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 477": "OE1" <-> "OE2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 32393 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'CIS': 1, 'TRANS': 212, 'PCIS': 1} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PTRANS': 55, 'CIS': 3, 'TRANS': 1280, 'PCIS': 1} Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 55, 'CIS': 1, 'TRANS': 1279} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3847 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1402 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "Q" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1386 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 68, 'PCIS': 1} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14538 SG CYS J 70 101.623 65.647 72.592 1.00101.34 S ATOM 14552 SG CYS J 72 99.864 64.175 69.772 1.00105.00 S ATOM 14660 SG CYS J 85 103.554 65.828 69.277 1.00104.39 S ATOM 14684 SG CYS J 88 100.156 66.070 70.354 1.00102.11 S ATOM 20372 SG CYS J 814 126.393 119.526 106.314 1.00 97.75 S ATOM 20937 SG CYS J 888 123.108 118.015 105.077 1.00 94.17 S ATOM 20988 SG CYS J 895 124.740 116.913 108.396 1.00 87.63 S ATOM 21009 SG CYS J 898 123.059 120.149 108.148 1.00 86.42 S Time building chain proxies: 17.75, per 1000 atoms: 0.55 Number of scatterers: 32393 At special positions: 0 Unit cell: (154.76, 193.98, 191.86, 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 130 16.00 P 136 15.00 Mg 1 11.99 O 6491 8.00 N 5727 7.00 C 19906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 37 sheets defined 36.6% alpha, 9.0% beta 53 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 11.72 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 85 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 232 removed outlier: 4.075A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 289 through 292 Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 removed outlier: 3.761A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.609A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 677 through 685 Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 861 through 864 removed outlier: 3.953A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 861 through 864' Processing helix chain 'I' and resid 897 through 906 Processing helix chain 'I' and resid 943 through 980 Processing helix chain 'I' and resid 994 through 996 No H-bonds generated for 'chain 'I' and resid 994 through 996' Processing helix chain 'I' and resid 1008 through 1037 removed outlier: 4.831A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 4.235A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.646A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.790A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.529A pdb=" N SER J 191 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 333 through 335 No H-bonds generated for 'chain 'J' and resid 333 through 335' Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 395 through 402 Processing helix chain 'J' and resid 409 through 415 Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 3.668A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR J 457 " --> pdb=" O CYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.787A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 599 through 612 removed outlier: 3.900A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.888A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 5.587A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1072 No H-bonds generated for 'chain 'J' and resid 1069 through 1072' Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.234A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.649A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1313 Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1329 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 77 Processing helix chain 'L' and resid 99 through 107 removed outlier: 4.258A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 136 removed outlier: 3.966A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 215 through 233 removed outlier: 5.626A pdb=" N ALA L 222 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU L 223 " --> pdb=" O ARG L 218 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU L 224 " --> pdb=" O GLU L 219 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG L 225 " --> pdb=" O LYS L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 258 Processing helix chain 'L' and resid 263 through 289 Processing helix chain 'L' and resid 299 through 306 Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 325 through 332 removed outlier: 4.726A pdb=" N HIS L 331 " --> pdb=" O SER L 327 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP L 332 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 393 removed outlier: 6.005A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 446 Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.919A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET L 474 " --> pdb=" O MET L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 removed outlier: 3.668A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 493 through 498 Processing helix chain 'L' and resid 519 through 521 No H-bonds generated for 'chain 'L' and resid 519 through 521' Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.586A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 604 through 610 removed outlier: 4.121A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 260 Processing helix chain 'R' and resid 264 through 272 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 286 through 290 Processing helix chain 'R' and resid 297 through 309 Processing sheet with id= A, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.903A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'G' and resid 97 through 99 Processing sheet with id= D, first strand: chain 'G' and resid 102 through 105 Processing sheet with id= E, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.731A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.624A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.644A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 109 through 111 removed outlier: 3.872A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.546A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= L, first strand: chain 'I' and resid 116 through 123 removed outlier: 3.850A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= N, first strand: chain 'I' and resid 173 through 175 Processing sheet with id= O, first strand: chain 'I' and resid 227 through 231 removed outlier: 3.532A pdb=" N ILE I 333 " --> pdb=" O PHE I 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= Q, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= R, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= S, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.765A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.615A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= V, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= W, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.801A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.278A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 816 through 818 removed outlier: 7.177A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.704A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.749A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.966A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AD, first strand: chain 'J' and resid 548 through 556 Processing sheet with id= AE, first strand: chain 'J' and resid 706 through 708 Processing sheet with id= AF, first strand: chain 'J' and resid 821 through 823 Processing sheet with id= AG, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.933A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AI, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 4.014A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AK, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.882A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 13.25 Time building geometry restraints manager: 13.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 5315 1.26 - 1.41: 7725 1.41 - 1.55: 19569 1.55 - 1.69: 318 1.69 - 1.83: 237 Bond restraints: 33164 Sorted by residual: bond pdb=" C17 1N7 Q 101 " pdb=" O3 1N7 Q 101 " ideal model delta sigma weight residual 0.000 1.409 -1.409 2.00e-02 2.50e+03 4.96e+03 bond pdb=" C17 1N7 I1402 " pdb=" O3 1N7 I1402 " ideal model delta sigma weight residual 0.000 1.408 -1.408 2.00e-02 2.50e+03 4.96e+03 bond pdb=" C17 1N7 I1401 " pdb=" O3 1N7 I1401 " ideal model delta sigma weight residual 0.000 1.402 -1.402 2.00e-02 2.50e+03 4.92e+03 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.261 1.735 -0.474 2.00e-02 2.50e+03 5.62e+02 bond pdb=" C18 1N7 Q 101 " pdb=" C6 1N7 Q 101 " ideal model delta sigma weight residual 0.987 1.450 -0.463 2.00e-02 2.50e+03 5.36e+02 ... (remaining 33159 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.97: 1063 104.97 - 112.23: 17167 112.23 - 119.50: 11157 119.50 - 126.76: 15339 126.76 - 134.03: 658 Bond angle restraints: 45384 Sorted by residual: angle pdb=" N GLU J 86 " pdb=" CA GLU J 86 " pdb=" C GLU J 86 " ideal model delta sigma weight residual 111.14 121.92 -10.78 1.08e+00 8.57e-01 9.96e+01 angle pdb=" N GLU J 713 " pdb=" CA GLU J 713 " pdb=" C GLU J 713 " ideal model delta sigma weight residual 110.53 122.51 -11.98 1.32e+00 5.74e-01 8.24e+01 angle pdb=" C GLU L 503 " pdb=" N PRO L 504 " pdb=" CA PRO L 504 " ideal model delta sigma weight residual 119.84 130.10 -10.26 1.25e+00 6.40e-01 6.74e+01 angle pdb=" C VAL J 90 " pdb=" CA VAL J 90 " pdb=" CB VAL J 90 " ideal model delta sigma weight residual 110.96 101.31 9.65 1.21e+00 6.83e-01 6.36e+01 angle pdb=" C ILE I1210 " pdb=" CA ILE I1210 " pdb=" CB ILE I1210 " ideal model delta sigma weight residual 111.29 98.50 12.79 1.64e+00 3.72e-01 6.08e+01 ... (remaining 45379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 18859 34.45 - 68.90: 995 68.90 - 103.36: 38 103.36 - 137.81: 0 137.81 - 172.26: 1 Dihedral angle restraints: 19893 sinusoidal: 9075 harmonic: 10818 Sorted by residual: dihedral pdb=" CA PHE J1325 " pdb=" C PHE J1325 " pdb=" N GLN J1326 " pdb=" CA GLN J1326 " ideal model delta harmonic sigma weight residual 180.00 136.30 43.70 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -143.95 -36.05 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA SER J 119 " pdb=" C SER J 119 " pdb=" N LEU J 120 " pdb=" CA LEU J 120 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 19890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 5173 0.294 - 0.587: 16 0.587 - 0.881: 3 0.881 - 1.174: 0 1.174 - 1.468: 3 Chirality restraints: 5195 Sorted by residual: chirality pdb=" C18 1N7 I1402 " pdb=" C17 1N7 I1402 " pdb=" C19 1N7 I1402 " pdb=" C6 1N7 I1402 " both_signs ideal model delta sigma weight residual False 1.21 2.68 -1.47 2.00e-01 2.50e+01 5.39e+01 chirality pdb=" C18 1N7 I1401 " pdb=" C17 1N7 I1401 " pdb=" C19 1N7 I1401 " pdb=" C6 1N7 I1401 " both_signs ideal model delta sigma weight residual False 1.21 2.66 -1.45 2.00e-01 2.50e+01 5.23e+01 chirality pdb=" C18 1N7 Q 101 " pdb=" C17 1N7 Q 101 " pdb=" C19 1N7 Q 101 " pdb=" C6 1N7 Q 101 " both_signs ideal model delta sigma weight residual False 1.21 2.65 -1.44 2.00e-01 2.50e+01 5.17e+01 ... (remaining 5192 not shown) Planarity restraints: 5427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J1325 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C PHE J1325 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE J1325 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN J1326 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 235 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ARG G 235 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG G 235 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP G 236 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 705 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C THR J 705 " -0.048 2.00e-02 2.50e+03 pdb=" O THR J 705 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL J 706 " 0.016 2.00e-02 2.50e+03 ... (remaining 5424 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 33 2.30 - 2.95: 14796 2.95 - 3.60: 45751 3.60 - 4.25: 72581 4.25 - 4.90: 122733 Nonbonded interactions: 255894 Sorted by model distance: nonbonded pdb=" NZ LYS J 74 " pdb=" NZ LYS J 87 " model vdw 1.653 3.200 nonbonded pdb=" O ASP I 516 " pdb=" OD1 ASP I 516 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR J 844 " pdb=" O ARG J 860 " model vdw 2.163 2.440 nonbonded pdb=" N ASP J 751 " pdb=" OD1 ASP J 751 " model vdw 2.165 2.520 nonbonded pdb=" O SER J 775 " pdb=" OG SER J 775 " model vdw 2.174 2.440 ... (remaining 255889 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' and (resid 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 136 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19906 2.51 5 N 5727 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.970 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.240 Process input model: 90.280 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.010 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.019 1.409 33164 Z= 1.088 Angle : 0.838 12.791 45384 Z= 0.490 Chirality : 0.067 1.468 5195 Planarity : 0.005 0.092 5427 Dihedral : 17.758 172.262 12917 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer Outliers : 6.15 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3732 helix: 0.30 (0.14), residues: 1450 sheet: -2.02 (0.24), residues: 444 loop : -1.93 (0.14), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 238 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 105 residues processed: 426 average time/residue: 0.4524 time to fit residues: 320.0214 Evaluate side-chains 315 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 210 time to evaluate : 3.759 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.2983 time to fit residues: 64.4783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 chunk 196 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 301 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 349 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 513 GLN I 554 HIS I 761 GLN I 798 GLN J 495 ASN J 720 ASN J 777 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 33164 Z= 0.231 Angle : 0.699 16.630 45384 Z= 0.359 Chirality : 0.044 0.299 5195 Planarity : 0.005 0.060 5427 Dihedral : 17.826 171.406 5481 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3732 helix: 0.51 (0.14), residues: 1464 sheet: -1.87 (0.24), residues: 432 loop : -1.87 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 26 residues processed: 277 average time/residue: 0.4344 time to fit residues: 194.6529 Evaluate side-chains 246 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 3.546 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3045 time to fit residues: 19.0741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 378 optimal weight: 0.0170 chunk 311 optimal weight: 5.9990 chunk 347 optimal weight: 5.9990 chunk 119 optimal weight: 0.4980 chunk 280 optimal weight: 8.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 798 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.822 33164 Z= 0.323 Angle : 0.728 33.079 45384 Z= 0.384 Chirality : 0.044 0.298 5195 Planarity : 0.005 0.154 5427 Dihedral : 17.826 171.406 5481 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3732 helix: 0.51 (0.14), residues: 1464 sheet: -1.87 (0.24), residues: 432 loop : -1.87 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.4619 time to fit residues: 167.5156 Evaluate side-chains 219 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 372 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 333 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 798 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.800 33164 Z= 0.319 Angle : 0.731 32.603 45384 Z= 0.384 Chirality : 0.044 0.297 5195 Planarity : 0.005 0.152 5427 Dihedral : 17.826 171.406 5481 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3732 helix: 0.51 (0.14), residues: 1464 sheet: -1.87 (0.24), residues: 432 loop : -1.87 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.4445 time to fit residues: 157.2293 Evaluate side-chains 220 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3194 time to fit residues: 5.1089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 30.0000 chunk 153 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 190 optimal weight: 0.5980 chunk 334 optimal weight: 40.0000 chunk 93 optimal weight: 0.0980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 798 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.742 33164 Z= 0.309 Angle : 0.729 31.316 45384 Z= 0.382 Chirality : 0.044 0.293 5195 Planarity : 0.005 0.148 5427 Dihedral : 17.826 171.407 5481 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3732 helix: 0.51 (0.14), residues: 1464 sheet: -1.87 (0.24), residues: 432 loop : -1.87 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.4761 time to fit residues: 169.2625 Evaluate side-chains 219 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 0.9980 chunk 335 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 372 optimal weight: 30.0000 chunk 309 optimal weight: 0.0770 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.125 33164 Z= 0.364 Angle : 0.696 15.146 45384 Z= 0.357 Chirality : 0.045 0.245 5195 Planarity : 0.005 0.083 5427 Dihedral : 17.800 171.807 5481 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3732 helix: 0.52 (0.14), residues: 1464 sheet: -1.86 (0.24), residues: 432 loop : -1.85 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 242 average time/residue: 0.4700 time to fit residues: 183.4738 Evaluate side-chains 235 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 3.581 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.3504 time to fit residues: 16.6718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 313 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.125 33164 Z= 0.364 Angle : 0.696 15.146 45384 Z= 0.357 Chirality : 0.045 0.245 5195 Planarity : 0.005 0.083 5427 Dihedral : 17.800 171.807 5481 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3732 helix: 0.52 (0.14), residues: 1464 sheet: -1.86 (0.24), residues: 432 loop : -1.85 (0.14), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.4714 time to fit residues: 167.1189 Evaluate side-chains 217 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 3.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.0042 time to fit residues: 6.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 72 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 291 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 33164 Z= 0.242 Angle : 0.659 15.417 45384 Z= 0.340 Chirality : 0.043 0.240 5195 Planarity : 0.005 0.077 5427 Dihedral : 17.786 171.847 5481 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.02 % Favored : 92.93 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3732 helix: 0.60 (0.14), residues: 1465 sheet: -1.82 (0.24), residues: 430 loop : -1.83 (0.14), residues: 1837 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 223 average time/residue: 0.4681 time to fit residues: 168.1214 Evaluate side-chains 225 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 3.525 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2826 time to fit residues: 9.0260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 30.0000 chunk 355 optimal weight: 2.9990 chunk 324 optimal weight: 30.0000 chunk 345 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 106 optimal weight: 0.4980 chunk 312 optimal weight: 7.9990 chunk 327 optimal weight: 9.9990 chunk 344 optimal weight: 0.0980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 33164 Z= 0.325 Angle : 0.661 15.106 45384 Z= 0.341 Chirality : 0.044 0.186 5195 Planarity : 0.005 0.094 5427 Dihedral : 17.775 171.864 5481 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3732 helix: 0.60 (0.14), residues: 1466 sheet: -1.83 (0.24), residues: 432 loop : -1.81 (0.14), residues: 1834 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 220 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 227 average time/residue: 0.4943 time to fit residues: 182.2106 Evaluate side-chains 218 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3330 time to fit residues: 8.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.0870 chunk 365 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 383 optimal weight: 2.9990 chunk 353 optimal weight: 7.9990 chunk 305 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 33164 Z= 0.325 Angle : 0.661 15.106 45384 Z= 0.341 Chirality : 0.044 0.186 5195 Planarity : 0.005 0.094 5427 Dihedral : 17.775 171.864 5481 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3732 helix: 0.60 (0.14), residues: 1466 sheet: -1.83 (0.24), residues: 432 loop : -1.81 (0.14), residues: 1834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.4707 time to fit residues: 162.7100 Evaluate side-chains 213 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 93 optimal weight: 0.0040 chunk 281 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 305 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.129519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.072573 restraints weight = 66664.417| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.16 r_work: 0.2915 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work: 0.2889 rms_B_bonded: 2.91 restraints_weight: 0.1250 r_work: 0.2876 rms_B_bonded: 2.94 restraints_weight: 0.0625 r_work: 0.2862 rms_B_bonded: 3.00 restraints_weight: 0.0312 r_work: 0.2848 rms_B_bonded: 3.08 restraints_weight: 0.0156 r_work: 0.2834 rms_B_bonded: 3.18 restraints_weight: 0.0078 r_work: 0.2820 rms_B_bonded: 3.29 restraints_weight: 0.0039 r_work: 0.2805 rms_B_bonded: 3.42 restraints_weight: 0.0020 r_work: 0.2790 rms_B_bonded: 3.57 restraints_weight: 0.0010 r_work: 0.2774 rms_B_bonded: 3.74 restraints_weight: 0.0005 r_work: 0.2758 rms_B_bonded: 3.93 restraints_weight: 0.0002 r_work: 0.2741 rms_B_bonded: 4.14 restraints_weight: 0.0001 r_work: 0.2723 rms_B_bonded: 4.37 restraints_weight: 0.0001 r_work: 0.2705 rms_B_bonded: 4.62 restraints_weight: 0.0000 r_work: 0.2687 rms_B_bonded: 4.90 restraints_weight: 0.0000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 33164 Z= 0.325 Angle : 0.661 15.106 45384 Z= 0.341 Chirality : 0.044 0.186 5195 Planarity : 0.005 0.094 5427 Dihedral : 17.775 171.864 5481 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3732 helix: 0.60 (0.14), residues: 1466 sheet: -1.83 (0.24), residues: 432 loop : -1.81 (0.14), residues: 1834 =============================================================================== Job complete usr+sys time: 5730.37 seconds wall clock time: 106 minutes 23.60 seconds (6383.60 seconds total)