Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 14:34:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6b_30118/04_2023/6m6b_30118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6b_30118/04_2023/6m6b_30118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6b_30118/04_2023/6m6b_30118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6b_30118/04_2023/6m6b_30118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6b_30118/04_2023/6m6b_30118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6b_30118/04_2023/6m6b_30118_updated.pdb" } resolution = 4.1 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= 0.001 sd= 0.008 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 59 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 17690 2.51 5 N 4998 2.21 5 O 5361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C ASP 617": "OD1" <-> "OD2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 766": "OE1" <-> "OE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 808": "NH1" <-> "NH2" Residue "C TYR 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 837": "OD1" <-> "OD2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "C GLU 1041": "OE1" <-> "OE2" Residue "C GLU 1061": "OE1" <-> "OE2" Residue "C GLU 1074": "OE1" <-> "OE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1091": "OE1" <-> "OE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 441": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D ARG 587": "NH1" <-> "NH2" Residue "D TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 832": "NH1" <-> "NH2" Residue "D PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 867": "NH1" <-> "NH2" Residue "D TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 872": "NH1" <-> "NH2" Residue "D TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 958": "OE1" <-> "OE2" Residue "D TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 968": "OD1" <-> "OD2" Residue "D GLU 979": "OE1" <-> "OE2" Residue "D TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1051": "OE1" <-> "OE2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1083": "OD1" <-> "OD2" Residue "D ARG 1087": "NH1" <-> "NH2" Residue "D ASP 1100": "OD1" <-> "OD2" Residue "D ARG 1108": "NH1" <-> "NH2" Residue "D TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1133": "NH1" <-> "NH2" Residue "D TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1151": "NH1" <-> "NH2" Residue "D TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1231": "OE1" <-> "OE2" Residue "D GLU 1261": "OE1" <-> "OE2" Residue "D TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1406": "NH1" <-> "NH2" Residue "D ASP 1488": "OD1" <-> "OD2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 817": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28180 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1782 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1750 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 207} Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8770 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1038} Chain breaks: 1 Chain: "D" Number of atoms: 10300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10300 Classifications: {'peptide': 1305} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1240} Chain breaks: 2 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "M" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3635 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 29, 'TRANS': 429} Chain breaks: 2 Chain: "T" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "N" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 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} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19686 SG CYS D1112 83.639 68.049 129.157 1.00143.09 S ATOM 20330 SG CYS D1194 82.345 68.479 125.745 1.00126.28 S ATOM 20386 SG CYS D1201 81.623 65.492 127.728 1.00136.20 S ATOM 20410 SG CYS D1204 79.425 68.601 129.001 1.00129.08 S Time building chain proxies: 13.92, per 1000 atoms: 0.49 Number of scatterers: 28180 At special positions: 0 Unit cell: (164.682, 141.156, 164.682, 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 69 16.00 P 59 15.00 Mg 1 11.99 O 5361 8.00 N 4998 7.00 C 17690 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: 11.94 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " Number of angles added : 6 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 41 sheets defined 34.3% alpha, 14.0% beta 30 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 11.16 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.637A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 44 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 153 through 156 No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 207 through 222 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 215 through 218 No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 225 through 228 No H-bonds generated for 'chain 'C' and resid 225 through 228' Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 303 through 314 Processing helix chain 'C' and resid 336 through 360 removed outlier: 3.810A pdb=" N LEU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 400 through 407 Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.396A pdb=" N ARG C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 555 through 567 removed outlier: 4.417A pdb=" N THR C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 590 Processing helix chain 'C' and resid 693 through 696 No H-bonds generated for 'chain 'C' and resid 693 through 696' Processing helix chain 'C' and resid 732 through 734 No H-bonds generated for 'chain 'C' and resid 732 through 734' Processing helix chain 'C' and resid 769 through 778 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 883 through 897 Processing helix chain 'C' and resid 911 through 931 removed outlier: 4.254A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 950 removed outlier: 3.683A pdb=" N LEU C 950 " --> pdb=" O ARG C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 969 Processing helix chain 'C' and resid 1024 through 1026 No H-bonds generated for 'chain 'C' and resid 1024 through 1026' Processing helix chain 'C' and resid 1034 through 1043 Processing helix chain 'C' and resid 1046 through 1053 Processing helix chain 'C' and resid 1061 through 1072 Processing helix chain 'C' and resid 1083 through 1095 Processing helix chain 'D' and resid 15 through 21 Processing helix chain 'D' and resid 47 through 50 No H-bonds generated for 'chain 'D' and resid 47 through 50' Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 423 through 425 No H-bonds generated for 'chain 'D' and resid 423 through 425' Processing helix chain 'D' and resid 458 through 467 removed outlier: 3.750A pdb=" N GLU D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 482 Processing helix chain 'D' and resid 486 through 505 Processing helix chain 'D' and resid 509 through 512 Processing helix chain 'D' and resid 523 through 525 No H-bonds generated for 'chain 'D' and resid 523 through 525' Processing helix chain 'D' and resid 539 through 560 removed outlier: 3.558A pdb=" N GLN D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 583 Processing helix chain 'D' and resid 603 through 607 Processing helix chain 'D' and resid 646 through 652 Processing helix chain 'D' and resid 654 through 663 Processing helix chain 'D' and resid 670 through 677 Processing helix chain 'D' and resid 680 through 682 No H-bonds generated for 'chain 'D' and resid 680 through 682' Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 710 through 712 No H-bonds generated for 'chain 'D' and resid 710 through 712' Processing helix chain 'D' and resid 730 through 732 No H-bonds generated for 'chain 'D' and resid 730 through 732' Processing helix chain 'D' and resid 753 through 762 removed outlier: 3.719A pdb=" N GLN D 762 " --> pdb=" O GLU D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 767 No H-bonds generated for 'chain 'D' and resid 765 through 767' Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 837 through 840 No H-bonds generated for 'chain 'D' and resid 837 through 840' Processing helix chain 'D' and resid 846 through 854 Processing helix chain 'D' and resid 877 through 890 Processing helix chain 'D' and resid 893 through 899 Processing helix chain 'D' and resid 908 through 922 Processing helix chain 'D' and resid 925 through 945 removed outlier: 3.569A pdb=" N SER D 945 " --> pdb=" O PHE D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 953 No H-bonds generated for 'chain 'D' and resid 951 through 953' Processing helix chain 'D' and resid 959 through 979 Processing helix chain 'D' and resid 985 through 1014 Processing helix chain 'D' and resid 1019 through 1026 Processing helix chain 'D' and resid 1032 through 1039 Processing helix chain 'D' and resid 1067 through 1101 removed outlier: 4.408A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1144 Processing helix chain 'D' and resid 1168 through 1180 Processing helix chain 'D' and resid 1221 through 1235 Proline residue: D1232 - end of helix removed outlier: 5.178A pdb=" N GLN D1235 " --> pdb=" O GLU D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1256 through 1264 Processing helix chain 'D' and resid 1332 through 1358 Proline residue: D1341 - end of helix removed outlier: 3.915A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1366 through 1377 removed outlier: 3.810A pdb=" N LYS D1377 " --> pdb=" O ARG D1373 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1408 Processing helix chain 'D' and resid 1424 through 1429 Processing helix chain 'D' and resid 1434 through 1440 Processing helix chain 'D' and resid 1443 through 1453 Processing helix chain 'D' and resid 1463 through 1467 Processing helix chain 'D' and resid 1475 through 1477 No H-bonds generated for 'chain 'D' and resid 1475 through 1477' Processing helix chain 'D' and resid 1490 through 1500 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 82 through 92 Processing helix chain 'M' and resid 365 through 367 No H-bonds generated for 'chain 'M' and resid 365 through 367' Processing helix chain 'M' and resid 408 through 419 Processing helix chain 'M' and resid 431 through 438 removed outlier: 3.687A pdb=" N VAL M 435 " --> pdb=" O TRP M 431 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 438 " --> pdb=" O LEU M 434 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 459 Processing helix chain 'M' and resid 476 through 489 removed outlier: 3.900A pdb=" N ALA M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 501 through 514 Processing helix chain 'M' and resid 531 through 542 Processing helix chain 'M' and resid 554 through 557 No H-bonds generated for 'chain 'M' and resid 554 through 557' Processing helix chain 'M' and resid 573 through 575 No H-bonds generated for 'chain 'M' and resid 573 through 575' Processing helix chain 'M' and resid 578 through 587 Processing helix chain 'M' and resid 606 through 612 removed outlier: 3.620A pdb=" N VAL M 610 " --> pdb=" O TYR M 606 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY M 611 " --> pdb=" O SER M 607 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU M 612 " --> pdb=" O ALA M 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 606 through 612' Processing helix chain 'M' and resid 637 through 650 Processing helix chain 'M' and resid 665 through 674 Processing helix chain 'M' and resid 689 through 701 Processing helix chain 'M' and resid 735 through 744 Processing helix chain 'M' and resid 764 through 774 Processing helix chain 'M' and resid 782 through 795 Processing helix chain 'M' and resid 812 through 824 removed outlier: 3.830A pdb=" N ILE M 823 " --> pdb=" O LEU M 819 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG M 824 " --> pdb=" O GLU M 820 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 10 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 96 through 104 removed outlier: 6.166A pdb=" N ASP A 145 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL A 53 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A 147 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR A 51 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= E, first strand: chain 'B' and resid 10 through 16 Processing sheet with id= F, first strand: chain 'B' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.708A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= I, first strand: chain 'C' and resid 91 through 93 Processing sheet with id= J, first strand: chain 'C' and resid 108 through 114 removed outlier: 3.860A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 127 through 129 Processing sheet with id= L, first strand: chain 'C' and resid 139 through 142 Processing sheet with id= M, first strand: chain 'C' and resid 145 through 150 removed outlier: 7.716A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 292 through 294 Processing sheet with id= O, first strand: chain 'C' and resid 469 through 472 Processing sheet with id= P, first strand: chain 'C' and resid 495 through 497 Processing sheet with id= Q, first strand: chain 'C' and resid 620 through 624 removed outlier: 5.913A pdb=" N ARG C 614 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL C 603 " --> pdb=" O ARG C 614 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 869 through 871 removed outlier: 3.647A pdb=" N ALA C 840 " --> pdb=" O MET C 995 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 759 through 761 Processing sheet with id= T, first strand: chain 'C' and resid 688 through 691 removed outlier: 7.704A pdb=" N ILE C 690 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE C 852 " --> pdb=" O ILE C 690 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.545A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 91 through 94 Processing sheet with id= W, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.692A pdb=" N GLY D 201 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 398 through 402 Processing sheet with id= Y, first strand: chain 'D' and resid 626 through 630 Processing sheet with id= Z, first strand: chain 'D' and resid 631 through 633 removed outlier: 6.184A pdb=" N ILE D 726 " --> pdb=" O VAL D 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 641 through 645 removed outlier: 6.109A pdb=" N GLN D 717 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU D 644 " --> pdb=" O GLN D 717 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL D 719 " --> pdb=" O LEU D 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 864 through 868 Processing sheet with id= AC, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id= AD, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id= AE, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id= AF, first strand: chain 'D' and resid 1317 through 1319 removed outlier: 3.624A pdb=" N ASP D1317 " --> pdb=" O VAL D1281 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 7.174A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 133 through 136 removed outlier: 7.322A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 419 through 422 removed outlier: 6.752A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id= AK, first strand: chain 'E' and resid 47 through 49 Processing sheet with id= AL, first strand: chain 'M' and resid 324 through 327 removed outlier: 6.693A pdb=" N VAL M 352 " --> pdb=" O LEU M 336 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU M 338 " --> pdb=" O TYR M 350 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR M 350 " --> pdb=" O LEU M 338 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY M 359 " --> pdb=" O TYR M 355 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 465 through 467 removed outlier: 7.085A pdb=" N THR M 593 " --> pdb=" O ARG M 466 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'M' and resid 494 through 497 Processing sheet with id= AO, first strand: chain 'M' and resid 629 through 633 removed outlier: 3.649A pdb=" N ALA M 754 " --> pdb=" O LYS M 629 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU M 756 " --> pdb=" O PHE M 631 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS M 653 " --> pdb=" O ASN M 723 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE M 725 " --> pdb=" O LYS M 653 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE M 655 " --> pdb=" O ILE M 725 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE M 727 " --> pdb=" O PHE M 655 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 13.49 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 9569 1.36 - 1.51: 8768 1.51 - 1.65: 10344 1.65 - 1.80: 106 1.80 - 1.94: 18 Bond restraints: 28805 Sorted by residual: bond pdb=" CA SER C 878 " pdb=" C SER C 878 " ideal model delta sigma weight residual 1.523 1.457 0.067 1.56e-02 4.11e+03 1.83e+01 bond pdb=" C PRO M 759 " pdb=" N PRO M 760 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.55e+01 bond pdb=" N VAL C 302 " pdb=" CA VAL C 302 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.33e+01 bond pdb=" N THR M 620 " pdb=" CA THR M 620 " ideal model delta sigma weight residual 1.457 1.485 -0.029 9.10e-03 1.21e+04 9.91e+00 bond pdb=" C THR M 620 " pdb=" O THR M 620 " ideal model delta sigma weight residual 1.233 1.248 -0.015 4.80e-03 4.34e+04 9.44e+00 ... (remaining 28800 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.10: 848 105.10 - 112.63: 15308 112.63 - 120.16: 11155 120.16 - 127.69: 11644 127.69 - 135.22: 256 Bond angle restraints: 39211 Sorted by residual: angle pdb=" O3' DT N 10 " pdb=" C3' DT N 10 " pdb=" C2' DT N 10 " ideal model delta sigma weight residual 111.50 98.44 13.06 1.50e+00 4.44e-01 7.59e+01 angle pdb=" O3' DG N 13 " pdb=" C3' DG N 13 " pdb=" C2' DG N 13 " ideal model delta sigma weight residual 111.50 99.17 12.33 1.50e+00 4.44e-01 6.76e+01 angle pdb=" C4' DG N 13 " pdb=" C3' DG N 13 " pdb=" O3' DG N 13 " ideal model delta sigma weight residual 110.00 121.86 -11.86 1.50e+00 4.44e-01 6.25e+01 angle pdb=" C2' DG N 13 " pdb=" C1' DG N 13 " pdb=" N9 DG N 13 " ideal model delta sigma weight residual 113.50 103.11 10.39 1.50e+00 4.44e-01 4.80e+01 angle pdb=" O3' DT N 9 " pdb=" C3' DT N 9 " pdb=" C2' DT N 9 " ideal model delta sigma weight residual 111.50 102.32 9.18 1.50e+00 4.44e-01 3.75e+01 ... (remaining 39206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.98: 15203 18.98 - 37.96: 1756 37.96 - 56.94: 417 56.94 - 75.93: 83 75.93 - 94.91: 15 Dihedral angle restraints: 17474 sinusoidal: 7663 harmonic: 9811 Sorted by residual: dihedral pdb=" CA ILE D1452 " pdb=" C ILE D1452 " pdb=" N ALA D1453 " pdb=" CA ALA D1453 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA M 633 " pdb=" C ALA M 633 " pdb=" N PRO M 634 " pdb=" CA PRO M 634 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 17471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3197 0.055 - 0.110: 979 0.110 - 0.164: 220 0.164 - 0.219: 25 0.219 - 0.274: 8 Chirality restraints: 4429 Sorted by residual: chirality pdb=" CB VAL M 683 " pdb=" CA VAL M 683 " pdb=" CG1 VAL M 683 " pdb=" CG2 VAL M 683 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE C 726 " pdb=" CA ILE C 726 " pdb=" CG1 ILE C 726 " pdb=" CG2 ILE C 726 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE C 21 " pdb=" CA ILE C 21 " pdb=" CG1 ILE C 21 " pdb=" CG2 ILE C 21 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4426 not shown) Planarity restraints: 4938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG N 13 " 0.061 2.00e-02 2.50e+03 2.92e-02 2.57e+01 pdb=" N9 DG N 13 " -0.075 2.00e-02 2.50e+03 pdb=" C8 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG N 13 " 0.028 2.00e-02 2.50e+03 pdb=" N1 DG N 13 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG N 13 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG N 13 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 621 " -0.061 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO M 622 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO M 622 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 622 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 172 " -0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO D 173 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " -0.048 5.00e-02 4.00e+02 ... (remaining 4935 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1184 2.69 - 3.24: 27029 3.24 - 3.79: 50223 3.79 - 4.35: 59985 4.35 - 4.90: 94657 Nonbonded interactions: 233078 Sorted by model distance: nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D2003 " model vdw 2.133 2.170 nonbonded pdb=" OD2 ASP D 741 " pdb="MG MG D2003 " model vdw 2.143 2.170 nonbonded pdb=" O PRO D 39 " pdb="ZN ZN D2002 " model vdw 2.144 2.230 nonbonded pdb=" N GLU C1083 " pdb=" OE1 GLU C1083 " model vdw 2.187 2.520 nonbonded pdb=" CG2 THR C1054 " pdb=" OE2 GLU C1083 " model vdw 2.222 3.460 ... (remaining 233073 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 'A' and resid 7 through 228) selection = chain 'B' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 4.130 Check model and map are aligned: 0.470 Set scattering table: 0.210 Process input model: 83.750 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.007 0.075 28805 Z= 0.479 Angle : 0.952 13.065 39211 Z= 0.560 Chirality : 0.055 0.274 4429 Planarity : 0.008 0.091 4938 Dihedral : 16.851 94.906 11168 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.12), residues: 3395 helix: -2.04 (0.11), residues: 1212 sheet: -2.25 (0.21), residues: 504 loop : -2.39 (0.13), residues: 1679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 503 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 512 average time/residue: 0.5000 time to fit residues: 381.5801 Evaluate side-chains 246 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 3.425 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2630 time to fit residues: 7.6754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 311 optimal weight: 0.1980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 212 ASN B 139 ASN ** C 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 829 GLN C 860 HIS C 889 HIS C 899 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 575 GLN D 724 GLN D 744 GLN D 748 HIS D 906 GLN ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1172 HIS D1195 GLN D1323 GLN ** D1374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 HIS ** M 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 574 HIS M 783 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 28805 Z= 0.192 Angle : 0.600 9.563 39211 Z= 0.314 Chirality : 0.044 0.216 4429 Planarity : 0.006 0.057 4938 Dihedral : 13.714 91.980 4350 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3395 helix: -0.66 (0.14), residues: 1219 sheet: -1.84 (0.22), residues: 493 loop : -1.82 (0.14), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 380 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 384 average time/residue: 0.4422 time to fit residues: 263.6026 Evaluate side-chains 229 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2453 time to fit residues: 6.3963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 337 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 309 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN C 434 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN D 906 GLN D1005 GLN ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 28805 Z= 0.315 Angle : 0.639 9.480 39211 Z= 0.332 Chirality : 0.044 0.177 4429 Planarity : 0.006 0.059 4938 Dihedral : 13.523 88.927 4350 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3395 helix: -0.08 (0.14), residues: 1231 sheet: -1.64 (0.22), residues: 513 loop : -1.63 (0.15), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 320 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 324 average time/residue: 0.4330 time to fit residues: 220.4214 Evaluate side-chains 219 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 3.047 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2364 time to fit residues: 5.5751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 50.0000 chunk 234 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 331 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 296 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 213 GLN C 498 GLN C 899 GLN C1006 HIS ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 GLN ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 GLN ** D1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 516 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 28805 Z= 0.326 Angle : 0.629 9.670 39211 Z= 0.327 Chirality : 0.045 0.313 4429 Planarity : 0.005 0.055 4938 Dihedral : 13.495 88.159 4350 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3395 helix: 0.16 (0.14), residues: 1230 sheet: -1.59 (0.22), residues: 511 loop : -1.49 (0.15), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 299 average time/residue: 0.4410 time to fit residues: 209.2562 Evaluate side-chains 213 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 3.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2520 time to fit residues: 4.9694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 282 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 83 optimal weight: 0.4980 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN C 498 GLN C1006 HIS C1100 GLN D 507 ASN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 GLN ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1442 ASN E 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 28805 Z= 0.177 Angle : 0.555 9.401 39211 Z= 0.288 Chirality : 0.043 0.196 4429 Planarity : 0.005 0.053 4938 Dihedral : 13.342 86.473 4350 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3395 helix: 0.48 (0.15), residues: 1221 sheet: -1.40 (0.22), residues: 517 loop : -1.29 (0.15), residues: 1657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 306 average time/residue: 0.4401 time to fit residues: 213.5765 Evaluate side-chains 216 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 3.649 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3266 time to fit residues: 5.4264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 331 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 0.2980 chunk 174 optimal weight: 40.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN C1006 HIS D 744 GLN ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 28805 Z= 0.261 Angle : 0.581 9.707 39211 Z= 0.302 Chirality : 0.043 0.183 4429 Planarity : 0.005 0.051 4938 Dihedral : 13.316 86.664 4350 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.97 (0.14), residues: 3395 helix: 0.55 (0.15), residues: 1221 sheet: -1.38 (0.22), residues: 525 loop : -1.28 (0.15), residues: 1649 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.4039 time to fit residues: 191.1021 Evaluate side-chains 212 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 20.0000 chunk 37 optimal weight: 0.0870 chunk 189 optimal weight: 0.0980 chunk 242 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 185 optimal weight: 30.0000 chunk 330 optimal weight: 30.0000 chunk 206 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 HIS ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 28805 Z= 0.219 Angle : 0.569 9.271 39211 Z= 0.294 Chirality : 0.043 0.186 4429 Planarity : 0.005 0.052 4938 Dihedral : 13.262 86.807 4350 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.89 (0.14), residues: 3395 helix: 0.60 (0.15), residues: 1221 sheet: -1.29 (0.22), residues: 535 loop : -1.23 (0.16), residues: 1639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.4160 time to fit residues: 199.5005 Evaluate side-chains 211 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 210 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 300 optimal weight: 30.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN C1006 HIS ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28805 Z= 0.195 Angle : 0.563 9.261 39211 Z= 0.290 Chirality : 0.043 0.192 4429 Planarity : 0.005 0.054 4938 Dihedral : 13.199 86.754 4350 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.81 (0.14), residues: 3395 helix: 0.64 (0.15), residues: 1229 sheet: -1.19 (0.22), residues: 517 loop : -1.20 (0.15), residues: 1649 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.4037 time to fit residues: 195.2282 Evaluate side-chains 212 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 28805 Z= 0.241 Angle : 0.588 16.080 39211 Z= 0.302 Chirality : 0.044 0.214 4429 Planarity : 0.005 0.052 4938 Dihedral : 13.167 86.984 4350 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.76 (0.15), residues: 3395 helix: 0.66 (0.15), residues: 1225 sheet: -1.08 (0.22), residues: 528 loop : -1.18 (0.16), residues: 1642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.4183 time to fit residues: 198.5129 Evaluate side-chains 207 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 341 optimal weight: 20.0000 chunk 314 optimal weight: 40.0000 chunk 272 optimal weight: 1.9990 chunk 28 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 91 ASN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 HIS ** C1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 783 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 28805 Z= 0.172 Angle : 0.569 19.553 39211 Z= 0.290 Chirality : 0.043 0.204 4429 Planarity : 0.005 0.053 4938 Dihedral : 13.091 86.873 4350 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.64 (0.15), residues: 3395 helix: 0.77 (0.15), residues: 1226 sheet: -1.00 (0.23), residues: 524 loop : -1.11 (0.16), residues: 1645 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.4152 time to fit residues: 202.1676 Evaluate side-chains 212 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 272 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 38 ASN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 HIS ** D1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102100 restraints weight = 67981.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096927 restraints weight = 63141.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098105 restraints weight = 70309.498| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28805 Z= 0.212 Angle : 0.573 13.534 39211 Z= 0.294 Chirality : 0.043 0.209 4429 Planarity : 0.005 0.054 4938 Dihedral : 13.063 86.923 4350 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.66 (0.15), residues: 3395 helix: 0.74 (0.15), residues: 1226 sheet: -0.96 (0.23), residues: 532 loop : -1.14 (0.15), residues: 1637 =============================================================================== Job complete usr+sys time: 5071.26 seconds wall clock time: 94 minutes 7.72 seconds (5647.72 seconds total)