Starting phenix.real_space_refine on Fri Feb 16 04:02:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/02_2024/7s9v_24938_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/02_2024/7s9v_24938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/02_2024/7s9v_24938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/02_2024/7s9v_24938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/02_2024/7s9v_24938_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/02_2024/7s9v_24938_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 73 5.16 5 C 8981 2.51 5 N 2558 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 635": "OD1" <-> "OD2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ASP 948": "OD1" <-> "OD2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A TYR 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1155": "OE1" <-> "OE2" Residue "A TYR 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1196": "OE1" <-> "OE2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A GLU 1230": "OE1" <-> "OE2" Residue "A GLU 1239": "OE1" <-> "OE2" Residue "A ASP 1285": "OD1" <-> "OD2" Residue "A PHE 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1314": "OD1" <-> "OD2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14286 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1296, 10121 Classifications: {'peptide': 1296} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1227} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4138 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 491} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.46, per 1000 atoms: 0.52 Number of scatterers: 14286 At special positions: 0 Unit cell: (95.7, 125.4, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 2 15.00 O 2672 8.00 N 2558 7.00 C 8981 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: 4.73 Conformation dependent library (CDL) restraints added in 2.6 seconds 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 20 sheets defined 30.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 109 through 118 Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.581A pdb=" N GLU A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 181' Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 343 through 346 removed outlier: 4.006A pdb=" N ALA A 346 " --> pdb=" O ARG A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 462 through 482 removed outlier: 4.139A pdb=" N VAL A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 520 removed outlier: 4.004A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 550 removed outlier: 4.438A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 570 through 583 Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 610 through 627 removed outlier: 3.862A pdb=" N GLY A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 618 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 676 removed outlier: 4.098A pdb=" N GLN A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.617A pdb=" N ILE A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 786 through 789 No H-bonds generated for 'chain 'A' and resid 786 through 789' Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.532A pdb=" N ALA A 805 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 807 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 808 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 4.166A pdb=" N ARG A 814 " --> pdb=" O GLY A 811 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 815 " --> pdb=" O GLN A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 873 through 889 removed outlier: 4.161A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 964 through 986 removed outlier: 3.695A pdb=" N HIS A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 Proline residue: A 992 - end of helix Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.739A pdb=" N ARG A1011 " --> pdb=" O GLY A1007 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN A1018 " --> pdb=" O GLU A1014 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A1019 " --> pdb=" O ASP A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Proline residue: A1055 - end of helix Processing helix chain 'A' and resid 1118 through 1126 Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1154 through 1157 No H-bonds generated for 'chain 'A' and resid 1154 through 1157' Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1175 through 1191 removed outlier: 3.974A pdb=" N ARG A1180 " --> pdb=" O ARG A1176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR A1183 " --> pdb=" O ASP A1179 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A1184 " --> pdb=" O ARG A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1205 Processing helix chain 'A' and resid 1211 through 1229 Processing helix chain 'A' and resid 1232 through 1253 removed outlier: 3.669A pdb=" N GLU A1252 " --> pdb=" O GLU A1248 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1253 " --> pdb=" O TRP A1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 53 through 63 removed outlier: 4.054A pdb=" N ALA B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.985A pdb=" N ALA B 126 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 211 through 214 removed outlier: 3.545A pdb=" N ALA B 214 " --> pdb=" O MET B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.577A pdb=" N TRP B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.846A pdb=" N SER B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.634A pdb=" N MET B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 535 through 540 removed outlier: 4.021A pdb=" N LEU B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 535 through 540' Processing helix chain 'B' and resid 542 through 557 removed outlier: 4.073A pdb=" N GLY B 546 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.742A pdb=" N ALA A 16 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 53 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 81 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 35 Processing sheet with id= C, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.545A pdb=" N TRP A 257 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 255 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 396 through 399 removed outlier: 3.871A pdb=" N LEU A 330 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 424 through 427 removed outlier: 3.510A pdb=" N TYR A 425 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A1134 " --> pdb=" O ARG A 953 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU A 955 " --> pdb=" O GLY A1134 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A1136 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 957 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A1138 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 924 through 928 removed outlier: 3.613A pdb=" N TRP A 603 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 903 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 600 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 800 " --> pdb=" O TRP A 691 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 743 through 745 Processing sheet with id= H, first strand: chain 'A' and resid 892 through 894 removed outlier: 3.506A pdb=" N TRP A 892 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.325A pdb=" N MET A 996 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA A1093 " --> pdb=" O MET A 996 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY A 998 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 999 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1068 through 1070 Processing sheet with id= K, first strand: chain 'A' and resid 1259 through 1261 Processing sheet with id= L, first strand: chain 'A' and resid 402 through 407 removed outlier: 3.916A pdb=" N GLU A 416 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= N, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.656A pdb=" N VAL B 419 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.594A pdb=" N SER B 110 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 148 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS B 134 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA B 150 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 132 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 13.439A pdb=" N ARG B 130 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 130 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 244 through 248 Processing sheet with id= Q, first strand: chain 'B' and resid 184 through 187 removed outlier: 3.671A pdb=" N ARG B 201 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 381 through 386 removed outlier: 3.790A pdb=" N ASN B 422 " --> pdb=" O ASN B 385 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 503 through 508 removed outlier: 3.904A pdb=" N ARG B 374 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET B 358 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 256 through 259 removed outlier: 4.089A pdb=" N GLY B 389 " --> pdb=" O ILE B 258 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4771 1.34 - 1.46: 2178 1.46 - 1.57: 7525 1.57 - 1.69: 3 1.69 - 1.81: 116 Bond restraints: 14593 Sorted by residual: bond pdb=" CB PRO A 929 " pdb=" CG PRO A 929 " ideal model delta sigma weight residual 1.506 1.410 0.096 3.90e-02 6.57e+02 6.00e+00 bond pdb=" C TRP B 19 " pdb=" N THR B 20 " ideal model delta sigma weight residual 1.333 1.302 0.031 1.34e-02 5.57e+03 5.37e+00 bond pdb=" CB ARG A 418 " pdb=" CG ARG A 418 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.07e+00 bond pdb=" CB ILE B 431 " pdb=" CG2 ILE B 431 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.65e+00 bond pdb=" CA TYR A 168 " pdb=" CB TYR A 168 " ideal model delta sigma weight residual 1.534 1.497 0.037 2.33e-02 1.84e+03 2.53e+00 ... (remaining 14588 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.59: 382 105.59 - 113.18: 7823 113.18 - 120.77: 6597 120.77 - 128.35: 4860 128.35 - 135.94: 130 Bond angle restraints: 19792 Sorted by residual: angle pdb=" N PRO A 211 " pdb=" CA PRO A 211 " pdb=" CB PRO A 211 " ideal model delta sigma weight residual 103.44 109.92 -6.48 1.12e+00 7.97e-01 3.35e+01 angle pdb=" C ARG B 71 " pdb=" N MET B 72 " pdb=" CA MET B 72 " ideal model delta sigma weight residual 121.03 129.07 -8.04 1.60e+00 3.91e-01 2.52e+01 angle pdb=" N ASP B 562 " pdb=" CA ASP B 562 " pdb=" C ASP B 562 " ideal model delta sigma weight residual 109.81 118.90 -9.09 2.21e+00 2.05e-01 1.69e+01 angle pdb=" N GLU A 482 " pdb=" CA GLU A 482 " pdb=" CB GLU A 482 " ideal model delta sigma weight residual 110.41 116.79 -6.38 1.68e+00 3.54e-01 1.44e+01 angle pdb=" N GLU A 988 " pdb=" CA GLU A 988 " pdb=" C GLU A 988 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 ... (remaining 19787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 7950 17.08 - 34.15: 726 34.15 - 51.23: 131 51.23 - 68.30: 29 68.30 - 85.37: 14 Dihedral angle restraints: 8850 sinusoidal: 3599 harmonic: 5251 Sorted by residual: dihedral pdb=" CA SER B 561 " pdb=" C SER B 561 " pdb=" N ASP B 562 " pdb=" CA ASP B 562 " ideal model delta harmonic sigma weight residual -180.00 -146.34 -33.66 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA ILE B 362 " pdb=" C ILE B 362 " pdb=" N GLY B 363 " pdb=" CA GLY B 363 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASP B 113 " pdb=" C ASP B 113 " pdb=" N ASP B 114 " pdb=" CA ASP B 114 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 8847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1478 0.048 - 0.097: 525 0.097 - 0.145: 154 0.145 - 0.194: 25 0.194 - 0.242: 4 Chirality restraints: 2186 Sorted by residual: chirality pdb=" CA ASP B 562 " pdb=" N ASP B 562 " pdb=" C ASP B 562 " pdb=" CB ASP B 562 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PRO A 211 " pdb=" N PRO A 211 " pdb=" C PRO A 211 " pdb=" CB PRO A 211 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2183 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 843 " 0.024 2.00e-02 2.50e+03 2.13e-02 7.94e+00 pdb=" CG PHE A 843 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 843 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 843 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 843 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 72 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO B 73 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 588 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 589 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.035 5.00e-02 4.00e+02 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3059 2.79 - 3.31: 11794 3.31 - 3.84: 20741 3.84 - 4.37: 23468 4.37 - 4.90: 43063 Nonbonded interactions: 102125 Sorted by model distance: nonbonded pdb=" OG1 THR A 611 " pdb=" O1B ADP A1401 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR B 183 " pdb=" OD2 ASP B 203 " model vdw 2.260 2.440 nonbonded pdb=" NH2 ARG A 370 " pdb=" OE2 GLU A 394 " model vdw 2.297 2.520 nonbonded pdb=" NH1 ARG A 814 " pdb=" O ASN A1194 " model vdw 2.303 2.520 nonbonded pdb=" OE1 GLU B 341 " pdb=" OH TYR B 508 " model vdw 2.306 2.440 ... (remaining 102120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.550 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 38.420 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 0.096 14593 Z= 0.452 Angle : 0.859 10.235 19792 Z= 0.476 Chirality : 0.054 0.242 2186 Planarity : 0.007 0.068 2599 Dihedral : 13.957 85.375 5456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.75 (0.18), residues: 1813 helix: -0.30 (0.22), residues: 500 sheet: -1.06 (0.31), residues: 287 loop : -1.66 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 892 HIS 0.014 0.001 HIS B 482 PHE 0.048 0.003 PHE A 843 TYR 0.025 0.003 TYR B 171 ARG 0.012 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5661 (tt0) cc_final: 0.4916 (mm110) REVERT: B 453 MET cc_start: 0.7948 (ttm) cc_final: 0.7713 (ttm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2975 time to fit residues: 62.7785 Evaluate side-chains 84 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14593 Z= 0.223 Angle : 0.583 10.036 19792 Z= 0.297 Chirality : 0.044 0.134 2186 Planarity : 0.005 0.055 2599 Dihedral : 5.165 43.665 2000 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.05 % Allowed : 5.85 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.19 (0.19), residues: 1813 helix: 0.55 (0.24), residues: 510 sheet: -0.82 (0.32), residues: 274 loop : -1.52 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 691 HIS 0.004 0.001 HIS B 482 PHE 0.016 0.001 PHE B 186 TYR 0.018 0.001 TYR A 614 ARG 0.008 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5383 (tt0) cc_final: 0.4624 (mm-40) REVERT: A 964 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7455 (mtp-110) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.2534 time to fit residues: 39.6285 Evaluate side-chains 92 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 ASN A 705 HIS A1112 ASN B 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14593 Z= 0.409 Angle : 0.663 7.205 19792 Z= 0.341 Chirality : 0.048 0.152 2186 Planarity : 0.006 0.049 2599 Dihedral : 5.297 37.047 2000 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.84 % Allowed : 9.60 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.37 (0.19), residues: 1813 helix: 0.37 (0.24), residues: 515 sheet: -1.00 (0.31), residues: 280 loop : -1.59 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.006 0.001 HIS A 268 PHE 0.017 0.002 PHE B 186 TYR 0.020 0.002 TYR A 614 ARG 0.004 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5462 (tt0) cc_final: 0.4846 (mm110) REVERT: A 964 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7000 (mtp-110) outliers start: 28 outliers final: 23 residues processed: 105 average time/residue: 0.2477 time to fit residues: 40.2369 Evaluate side-chains 102 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14593 Z= 0.164 Angle : 0.525 6.504 19792 Z= 0.268 Chirality : 0.043 0.134 2186 Planarity : 0.004 0.042 2599 Dihedral : 4.664 31.989 2000 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.51 % Allowed : 11.44 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.96 (0.19), residues: 1813 helix: 0.91 (0.24), residues: 511 sheet: -0.83 (0.32), residues: 268 loop : -1.42 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 281 HIS 0.011 0.001 HIS B 170 PHE 0.011 0.001 PHE A 571 TYR 0.020 0.001 TYR A 614 ARG 0.005 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5561 (tt0) cc_final: 0.4766 (mm-40) REVERT: A 162 MET cc_start: 0.8292 (ptm) cc_final: 0.8072 (ptm) REVERT: A 964 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6593 (mtp-110) REVERT: A 1112 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7594 (t0) outliers start: 23 outliers final: 10 residues processed: 100 average time/residue: 0.2365 time to fit residues: 37.9242 Evaluate side-chains 89 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 383 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 157 optimal weight: 0.0030 chunk 44 optimal weight: 5.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14593 Z= 0.166 Angle : 0.511 6.516 19792 Z= 0.259 Chirality : 0.043 0.134 2186 Planarity : 0.004 0.040 2599 Dihedral : 4.401 29.610 2000 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.10 % Allowed : 11.90 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.75 (0.20), residues: 1813 helix: 1.05 (0.24), residues: 522 sheet: -0.79 (0.32), residues: 270 loop : -1.27 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.002 0.001 HIS A 399 PHE 0.011 0.001 PHE A 571 TYR 0.019 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5584 (tt0) cc_final: 0.4826 (mm-40) REVERT: A 162 MET cc_start: 0.8337 (ptm) cc_final: 0.8121 (ptm) REVERT: A 964 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6448 (mtp-110) REVERT: A 1112 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7584 (t0) outliers start: 32 outliers final: 25 residues processed: 105 average time/residue: 0.2322 time to fit residues: 38.7051 Evaluate side-chains 104 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 175 optimal weight: 0.0050 chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14593 Z= 0.125 Angle : 0.482 6.887 19792 Z= 0.241 Chirality : 0.042 0.133 2186 Planarity : 0.004 0.039 2599 Dihedral : 4.109 27.267 2000 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.97 % Allowed : 12.36 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.51 (0.20), residues: 1813 helix: 1.28 (0.25), residues: 526 sheet: -0.67 (0.32), residues: 270 loop : -1.14 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.000 HIS A 705 PHE 0.009 0.001 PHE A 571 TYR 0.019 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5503 (tt0) cc_final: 0.4823 (mm-40) REVERT: A 162 MET cc_start: 0.8322 (ptm) cc_final: 0.8120 (ptm) outliers start: 30 outliers final: 26 residues processed: 110 average time/residue: 0.2543 time to fit residues: 43.7233 Evaluate side-chains 107 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.0570 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14593 Z= 0.163 Angle : 0.494 6.644 19792 Z= 0.247 Chirality : 0.042 0.132 2186 Planarity : 0.004 0.039 2599 Dihedral : 4.037 24.573 2000 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.04 % Allowed : 12.75 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.46 (0.20), residues: 1813 helix: 1.27 (0.25), residues: 528 sheet: -0.67 (0.32), residues: 274 loop : -1.08 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.002 0.001 HIS A 399 PHE 0.012 0.001 PHE A 571 TYR 0.018 0.001 TYR A 614 ARG 0.003 0.000 ARG A 964 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5485 (tt0) cc_final: 0.4757 (mm-40) outliers start: 31 outliers final: 29 residues processed: 108 average time/residue: 0.2498 time to fit residues: 43.2734 Evaluate side-chains 108 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 79 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14593 Z= 0.155 Angle : 0.485 7.115 19792 Z= 0.243 Chirality : 0.042 0.132 2186 Planarity : 0.004 0.038 2599 Dihedral : 3.960 22.625 2000 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.24 % Allowed : 13.02 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1813 helix: 1.36 (0.25), residues: 526 sheet: -0.55 (0.31), residues: 293 loop : -1.03 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.004 0.001 HIS A 705 PHE 0.011 0.001 PHE A 571 TYR 0.018 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5470 (tt0) cc_final: 0.4749 (mm-40) REVERT: B 600 ASP cc_start: 0.7373 (t70) cc_final: 0.6958 (t70) outliers start: 34 outliers final: 28 residues processed: 111 average time/residue: 0.2522 time to fit residues: 43.8988 Evaluate side-chains 108 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 0.9980 chunk 152 optimal weight: 0.0170 chunk 162 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.0370 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 171 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14593 Z= 0.129 Angle : 0.471 7.518 19792 Z= 0.234 Chirality : 0.042 0.134 2186 Planarity : 0.004 0.038 2599 Dihedral : 3.817 21.346 2000 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.17 % Allowed : 12.89 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.26 (0.20), residues: 1813 helix: 1.43 (0.25), residues: 526 sheet: -0.48 (0.31), residues: 293 loop : -0.97 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.004 0.000 HIS A 705 PHE 0.010 0.001 PHE A 571 TYR 0.018 0.001 TYR A 614 ARG 0.004 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5500 (tt0) cc_final: 0.4802 (mm-40) REVERT: A 1190 MET cc_start: 0.8118 (tpp) cc_final: 0.7874 (tpp) outliers start: 33 outliers final: 31 residues processed: 109 average time/residue: 0.2408 time to fit residues: 41.4446 Evaluate side-chains 111 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 0.0010 chunk 119 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14593 Z= 0.164 Angle : 0.488 7.510 19792 Z= 0.243 Chirality : 0.042 0.132 2186 Planarity : 0.004 0.038 2599 Dihedral : 3.884 19.997 2000 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.17 % Allowed : 12.69 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.28 (0.20), residues: 1813 helix: 1.39 (0.25), residues: 526 sheet: -0.48 (0.32), residues: 283 loop : -0.97 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.003 0.001 HIS A 705 PHE 0.012 0.001 PHE A 571 TYR 0.018 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5431 (tt0) cc_final: 0.4737 (mm-40) outliers start: 33 outliers final: 32 residues processed: 109 average time/residue: 0.2477 time to fit residues: 42.7575 Evaluate side-chains 109 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 943 GLN Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 573 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 143 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087567 restraints weight = 28059.966| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.82 r_work: 0.3173 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14593 Z= 0.133 Angle : 0.472 8.154 19792 Z= 0.234 Chirality : 0.042 0.133 2186 Planarity : 0.004 0.038 2599 Dihedral : 3.762 20.008 2000 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.10 % Allowed : 12.89 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.20 (0.20), residues: 1813 helix: 1.48 (0.25), residues: 525 sheet: -0.43 (0.32), residues: 288 loop : -0.93 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.004 0.000 HIS A 705 PHE 0.011 0.001 PHE A 843 TYR 0.018 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.48 seconds wall clock time: 48 minutes 55.89 seconds (2935.89 seconds total)