Starting phenix.real_space_refine on Mon Mar 18 17:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/03_2024/7usc_26732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/03_2024/7usc_26732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/03_2024/7usc_26732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/03_2024/7usc_26732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/03_2024/7usc_26732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/03_2024/7usc_26732.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 13831 2.51 5 N 3709 2.21 5 O 4023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A ARG 1049": "NH1" <-> "NH2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "B GLU 829": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B GLU 922": "OE1" <-> "OE2" Residue "B GLU 991": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E ARG 107": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21709 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9693 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 44, 'TRANS': 1138} Chain breaks: 6 Chain: "B" Number of atoms: 8716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8716 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 36, 'TRANS': 1050} Chain breaks: 3 Chain: "C" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain breaks: 2 Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 502 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1228 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Time building chain proxies: 10.57, per 1000 atoms: 0.49 Number of scatterers: 21709 At special positions: 0 Unit cell: (140.988, 141.863, 209.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 146 16.00 O 4023 8.00 N 3709 7.00 C 13831 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: 8.34 Conformation dependent library (CDL) restraints added in 4.1 seconds 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5176 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 7 sheets defined 77.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 Processing helix chain 'A' and resid 58 through 85 removed outlier: 4.057A pdb=" N GLN A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 144 removed outlier: 4.072A pdb=" N LYS A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.718A pdb=" N LYS A 150 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.656A pdb=" N ASN A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.653A pdb=" N LEU A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 3.649A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.517A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 4.153A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 5.366A pdb=" N SER A 330 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.532A pdb=" N GLU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.687A pdb=" N TYR A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 4.252A pdb=" N TYR A 443 " --> pdb=" O ARG A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.618A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.836A pdb=" N ARG A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.922A pdb=" N SER A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.578A pdb=" N ILE A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.563A pdb=" N ASN A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.616A pdb=" N CYS A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 5.654A pdb=" N GLN A 620 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 621 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 622 " --> pdb=" O SER A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 624 through 631 removed outlier: 3.596A pdb=" N THR A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 658 through 662 removed outlier: 4.304A pdb=" N GLU A 662 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 3.650A pdb=" N SER A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 722 removed outlier: 3.790A pdb=" N TYR A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 763 through 789 removed outlier: 3.617A pdb=" N LEU A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 793 No H-bonds generated for 'chain 'A' and resid 791 through 793' Processing helix chain 'A' and resid 794 through 814 removed outlier: 3.734A pdb=" N ARG A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 903 Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 910 through 942 removed outlier: 7.563A pdb=" N TYR A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 956 Processing helix chain 'A' and resid 964 through 967 Processing helix chain 'A' and resid 968 through 980 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 992 through 1026 removed outlier: 3.607A pdb=" N CYS A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1030 removed outlier: 3.771A pdb=" N ASN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1030' Processing helix chain 'A' and resid 1042 through 1055 Processing helix chain 'A' and resid 1058 through 1067 removed outlier: 3.722A pdb=" N LEU A1062 " --> pdb=" O HIS A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1084 removed outlier: 3.525A pdb=" N GLU A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1102 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.587A pdb=" N LEU A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1155 through 1168 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1200 through 1226 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.532A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.551A pdb=" N ILE B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.655A pdb=" N LYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.846A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 118 Processing helix chain 'B' and resid 126 through 149 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.522A pdb=" N LYS B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.673A pdb=" N MET B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.651A pdb=" N TYR B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 276 through 289 removed outlier: 3.512A pdb=" N LEU B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 313 removed outlier: 4.515A pdb=" N ASN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 360 removed outlier: 3.646A pdb=" N ASN B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 391 removed outlier: 3.526A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 removed outlier: 3.788A pdb=" N LEU B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 448 removed outlier: 3.759A pdb=" N MET B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.922A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 499 removed outlier: 3.799A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 508 removed outlier: 3.666A pdb=" N ASP B 508 " --> pdb=" O GLY B 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 509 through 528 removed outlier: 3.502A pdb=" N GLY B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.543A pdb=" N PHE B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.577A pdb=" N LEU B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.651A pdb=" N CYS B 573 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 580 removed outlier: 4.461A pdb=" N MET B 577 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 580 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 626 removed outlier: 4.708A pdb=" N HIS B 589 " --> pdb=" O PRO B 585 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 632 Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 673 through 690 removed outlier: 3.829A pdb=" N SER B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 724 removed outlier: 3.996A pdb=" N TYR B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 724 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 752 Processing helix chain 'B' and resid 753 through 756 Processing helix chain 'B' and resid 760 through 772 removed outlier: 3.923A pdb=" N VAL B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 795 Processing helix chain 'B' and resid 795 through 803 Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 832 through 872 Proline residue: B 845 - end of helix removed outlier: 3.803A pdb=" N HIS B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.743A pdb=" N ARG B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 932 removed outlier: 3.765A pdb=" N VAL B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 951 through 966 removed outlier: 3.596A pdb=" N ASN B 957 " --> pdb=" O LYS B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 979 Processing helix chain 'B' and resid 989 through 1006 Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 4.362A pdb=" N SER B1012 " --> pdb=" O PRO B1008 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1013' Processing helix chain 'B' and resid 1028 through 1030 No H-bonds generated for 'chain 'B' and resid 1028 through 1030' Processing helix chain 'B' and resid 1031 through 1047 Processing helix chain 'B' and resid 1050 through 1071 removed outlier: 3.893A pdb=" N GLN B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.821A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B1088 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP B1089 " --> pdb=" O TYR B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1107 removed outlier: 3.685A pdb=" N LEU B1103 " --> pdb=" O THR B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1121 removed outlier: 4.067A pdb=" N LEU B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 81 removed outlier: 3.948A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.576A pdb=" N PHE C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 177 Processing helix chain 'C' and resid 500 through 515 Processing helix chain 'C' and resid 530 through 543 Processing helix chain 'D' and resid 11 through 68 Processing helix chain 'E' and resid 4 through 39 removed outlier: 3.751A pdb=" N GLU E 10 " --> pdb=" O MET E 6 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Proline residue: E 13 - end of helix removed outlier: 3.874A pdb=" N ASP E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 110 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 308 removed outlier: 5.980A pdb=" N ILE A 313 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA3, first strand: chain 'A' and resid 855 through 858 Processing sheet with id=AA4, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AA5, first strand: chain 'B' and resid 695 through 697 Processing sheet with id=AA6, first strand: chain 'B' and resid 805 through 808 removed outlier: 3.502A pdb=" N ALA B 813 " --> pdb=" O PHE B 808 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1018 through 1019 1453 hydrogen bonds defined for protein. 4236 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: 7.68 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6965 1.33 - 1.45: 2765 1.45 - 1.57: 12161 1.57 - 1.69: 0 1.69 - 1.81: 237 Bond restraints: 22128 Sorted by residual: bond pdb=" C THR B 783 " pdb=" N ILE B 784 " ideal model delta sigma weight residual 1.335 1.243 0.091 1.15e-02 7.56e+03 6.31e+01 bond pdb=" C PRO C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 1.331 1.366 -0.034 8.70e-03 1.32e+04 1.57e+01 bond pdb=" N VAL B 300 " pdb=" CA VAL B 300 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N LEU A 569 " pdb=" CA LEU A 569 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ILE C 95 " pdb=" CA ILE C 95 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.14e+00 ... (remaining 22123 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.02: 381 106.02 - 113.03: 12112 113.03 - 120.04: 8339 120.04 - 127.05: 8843 127.05 - 134.06: 206 Bond angle restraints: 29881 Sorted by residual: angle pdb=" C PHE A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta sigma weight residual 119.85 124.83 -4.98 1.01e+00 9.80e-01 2.43e+01 angle pdb=" CA PRO C 131 " pdb=" C PRO C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 117.93 123.40 -5.47 1.20e+00 6.94e-01 2.08e+01 angle pdb=" C PHE A 164 " pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta sigma weight residual 120.46 114.35 6.11 1.37e+00 5.33e-01 1.99e+01 angle pdb=" N SER A 872 " pdb=" CA SER A 872 " pdb=" C SER A 872 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N VAL C 127 " pdb=" CA VAL C 127 " pdb=" C VAL C 127 " ideal model delta sigma weight residual 113.22 108.24 4.98 1.23e+00 6.61e-01 1.64e+01 ... (remaining 29876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12146 17.92 - 35.84: 1165 35.84 - 53.76: 197 53.76 - 71.68: 25 71.68 - 89.60: 18 Dihedral angle restraints: 13551 sinusoidal: 5610 harmonic: 7941 Sorted by residual: dihedral pdb=" CA ASN B 187 " pdb=" C ASN B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA PHE B1044 " pdb=" C PHE B1044 " pdb=" N THR B1045 " pdb=" CA THR B1045 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ASN B 873 " pdb=" C ASN B 873 " pdb=" N VAL B 874 " pdb=" CA VAL B 874 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 13548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2805 0.053 - 0.106: 470 0.106 - 0.160: 83 0.160 - 0.213: 10 0.213 - 0.266: 5 Chirality restraints: 3373 Sorted by residual: chirality pdb=" CA LEU C 92 " pdb=" N LEU C 92 " pdb=" C LEU C 92 " pdb=" CB LEU C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA HIS B 589 " pdb=" N HIS B 589 " pdb=" C HIS B 589 " pdb=" CB HIS B 589 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ILE A 570 " pdb=" N ILE A 570 " pdb=" C ILE A 570 " pdb=" CB ILE A 570 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3370 not shown) Planarity restraints: 3811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 783 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C THR B 783 " -0.067 2.00e-02 2.50e+03 pdb=" O THR B 783 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 784 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.031 2.00e-02 2.50e+03 2.56e-02 1.14e+01 pdb=" CG PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 149 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C ARG A 149 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 149 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 150 " -0.016 2.00e-02 2.50e+03 ... (remaining 3808 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 356 2.68 - 3.24: 22119 3.24 - 3.79: 33630 3.79 - 4.35: 45518 4.35 - 4.90: 76114 Nonbonded interactions: 177737 Sorted by model distance: nonbonded pdb=" O ASP A 427 " pdb=" OD1 ASP A 427 " model vdw 2.130 3.040 nonbonded pdb=" ND2 ASN B 33 " pdb=" OE1 GLU B 587 " model vdw 2.205 2.520 nonbonded pdb=" O LYS A 594 " pdb=" OE1 GLU A 598 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG A 964 " pdb=" OE1 GLN B 228 " model vdw 2.214 2.520 nonbonded pdb=" O ARG A 766 " pdb=" OG1 THR A 769 " model vdw 2.228 2.440 ... (remaining 177732 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: 1.760 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: 0.020 Extract box with map and model: 4.850 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 56.990 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.091 22128 Z= 0.445 Angle : 0.617 7.014 29881 Z= 0.378 Chirality : 0.043 0.266 3373 Planarity : 0.004 0.047 3811 Dihedral : 14.115 89.602 8375 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.16), residues: 2641 helix: 1.54 (0.12), residues: 1884 sheet: -3.24 (0.82), residues: 32 loop : -0.49 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 16 HIS 0.006 0.001 HIS A1128 PHE 0.059 0.002 PHE A 164 TYR 0.017 0.002 TYR B 430 ARG 0.006 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.906 Fit side-chains REVERT: A 82 MET cc_start: 0.9085 (tmm) cc_final: 0.8860 (tmm) REVERT: A 533 LEU cc_start: 0.8934 (mp) cc_final: 0.8714 (mm) REVERT: B 601 MET cc_start: 0.8222 (tmm) cc_final: 0.7750 (tmt) REVERT: C 109 GLN cc_start: 0.7665 (mt0) cc_final: 0.7257 (mt0) REVERT: D 49 THR cc_start: 0.9135 (m) cc_final: 0.8838 (p) REVERT: D 53 LYS cc_start: 0.8793 (tptt) cc_final: 0.8592 (mmmm) REVERT: E 108 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 1.7207 time to fit residues: 550.0336 Evaluate side-chains 195 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 135 optimal weight: 0.0000 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 241 optimal weight: 20.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 774 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22128 Z= 0.189 Angle : 0.509 10.108 29881 Z= 0.273 Chirality : 0.038 0.190 3373 Planarity : 0.004 0.044 3811 Dihedral : 3.734 19.807 2922 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.28 % Allowed : 7.50 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.17), residues: 2641 helix: 2.17 (0.12), residues: 1886 sheet: -2.52 (0.89), residues: 32 loop : -0.20 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS A1128 PHE 0.027 0.001 PHE B 549 TYR 0.021 0.001 TYR A1138 ARG 0.010 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 2.593 Fit side-chains revert: symmetry clash REVERT: A 150 LYS cc_start: 0.8761 (pptt) cc_final: 0.8557 (ptmm) REVERT: A 208 GLN cc_start: 0.8152 (tp40) cc_final: 0.7557 (tp40) REVERT: A 533 LEU cc_start: 0.8933 (mp) cc_final: 0.8718 (mm) REVERT: B 392 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6152 (pmm) REVERT: B 601 MET cc_start: 0.8146 (tmm) cc_final: 0.7938 (ttp) REVERT: D 49 THR cc_start: 0.9129 (m) cc_final: 0.8790 (p) REVERT: D 53 LYS cc_start: 0.8843 (tptt) cc_final: 0.8643 (mmmm) REVERT: E 6 MET cc_start: 0.7430 (tmm) cc_final: 0.6919 (tmm) REVERT: E 27 GLU cc_start: 0.8090 (tp30) cc_final: 0.7869 (tp30) REVERT: E 74 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: E 108 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6846 (mt-10) outliers start: 31 outliers final: 8 residues processed: 231 average time/residue: 1.6111 time to fit residues: 417.6019 Evaluate side-chains 199 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN C 109 GLN E 39 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22128 Z= 0.304 Angle : 0.520 16.881 29881 Z= 0.274 Chirality : 0.039 0.215 3373 Planarity : 0.004 0.045 3811 Dihedral : 3.646 20.730 2922 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.40 % Allowed : 9.56 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.40 (0.17), residues: 2641 helix: 2.30 (0.12), residues: 1883 sheet: -2.47 (0.86), residues: 32 loop : -0.09 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.023 0.001 PHE B 549 TYR 0.022 0.001 TYR A1138 ARG 0.005 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 2.811 Fit side-chains REVERT: A 104 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7328 (ttp-170) REVERT: A 208 GLN cc_start: 0.8199 (tp40) cc_final: 0.7682 (tp40) REVERT: A 533 LEU cc_start: 0.8967 (mp) cc_final: 0.8747 (mm) REVERT: B 305 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7981 (tptp) REVERT: B 392 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6199 (pmm) REVERT: D 49 THR cc_start: 0.9148 (m) cc_final: 0.8811 (p) REVERT: E 6 MET cc_start: 0.7550 (tmm) cc_final: 0.7314 (tmm) REVERT: E 36 ASN cc_start: 0.8550 (t0) cc_final: 0.8301 (t0) REVERT: E 74 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: E 87 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7677 (tm-30) outliers start: 34 outliers final: 15 residues processed: 219 average time/residue: 1.6508 time to fit residues: 405.6943 Evaluate side-chains 214 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 125 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 854 ASN B 161 ASN C 107 GLN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22128 Z= 0.176 Angle : 0.474 17.230 29881 Z= 0.249 Chirality : 0.037 0.187 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.501 19.212 2922 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.40 % Allowed : 10.63 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.70 (0.17), residues: 2641 helix: 2.53 (0.12), residues: 1879 sheet: -2.29 (0.86), residues: 32 loop : 0.03 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS A1128 PHE 0.016 0.001 PHE B 549 TYR 0.020 0.001 TYR A1138 ARG 0.005 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 2.548 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8138 (tp40) cc_final: 0.7572 (tp40) REVERT: A 533 LEU cc_start: 0.8974 (mp) cc_final: 0.8751 (mm) REVERT: B 305 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7898 (tptp) REVERT: E 36 ASN cc_start: 0.8537 (t0) cc_final: 0.8297 (t0) REVERT: E 87 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7705 (tm-30) outliers start: 34 outliers final: 14 residues processed: 213 average time/residue: 1.6130 time to fit residues: 383.7968 Evaluate side-chains 208 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22128 Z= 0.186 Angle : 0.476 16.829 29881 Z= 0.247 Chirality : 0.037 0.186 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.416 19.132 2922 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.19 % Allowed : 12.24 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.83 (0.17), residues: 2641 helix: 2.60 (0.12), residues: 1886 sheet: -2.18 (0.89), residues: 32 loop : 0.13 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS A1128 PHE 0.014 0.001 PHE B 549 TYR 0.027 0.001 TYR C 156 ARG 0.006 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 2.612 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8118 (tp40) cc_final: 0.7640 (tp40) REVERT: A 533 LEU cc_start: 0.8987 (mp) cc_final: 0.8773 (mm) REVERT: B 305 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7912 (tptp) REVERT: E 36 ASN cc_start: 0.8550 (t0) cc_final: 0.8308 (t0) REVERT: E 87 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7742 (tm-30) outliers start: 29 outliers final: 16 residues processed: 210 average time/residue: 1.5814 time to fit residues: 372.5454 Evaluate side-chains 212 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22128 Z= 0.297 Angle : 0.518 16.932 29881 Z= 0.268 Chirality : 0.039 0.189 3373 Planarity : 0.003 0.046 3811 Dihedral : 3.488 20.407 2922 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 12.77 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.72 (0.17), residues: 2641 helix: 2.52 (0.12), residues: 1886 sheet: -2.27 (0.88), residues: 32 loop : 0.09 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.019 0.001 PHE B1002 TYR 0.021 0.001 TYR A1138 ARG 0.007 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 2.679 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8144 (tp40) cc_final: 0.7647 (tp40) REVERT: A 533 LEU cc_start: 0.8999 (mp) cc_final: 0.8786 (mm) REVERT: B 305 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7982 (tptt) REVERT: E 36 ASN cc_start: 0.8559 (t0) cc_final: 0.8300 (t0) REVERT: E 87 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7680 (tm-30) outliers start: 35 outliers final: 18 residues processed: 220 average time/residue: 1.6153 time to fit residues: 397.4242 Evaluate side-chains 216 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 256 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22128 Z= 0.178 Angle : 0.479 17.011 29881 Z= 0.248 Chirality : 0.037 0.184 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.406 19.062 2922 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.11 % Allowed : 13.84 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.88 (0.17), residues: 2641 helix: 2.63 (0.12), residues: 1889 sheet: -2.18 (0.88), residues: 32 loop : 0.13 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.013 0.001 PHE A 391 TYR 0.028 0.001 TYR C 156 ARG 0.006 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8094 (tp40) cc_final: 0.7591 (tp40) REVERT: A 533 LEU cc_start: 0.9002 (mp) cc_final: 0.8788 (mm) REVERT: B 305 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7916 (tptp) REVERT: E 36 ASN cc_start: 0.8565 (t0) cc_final: 0.8316 (t0) REVERT: E 87 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7680 (tm-30) outliers start: 27 outliers final: 17 residues processed: 217 average time/residue: 1.5837 time to fit residues: 385.9226 Evaluate side-chains 215 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22128 Z= 0.305 Angle : 0.533 17.323 29881 Z= 0.275 Chirality : 0.039 0.189 3373 Planarity : 0.004 0.047 3811 Dihedral : 3.478 20.173 2922 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.32 % Allowed : 14.05 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.17), residues: 2641 helix: 2.55 (0.12), residues: 1879 sheet: -2.24 (0.88), residues: 32 loop : 0.08 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.017 0.001 PHE B1002 TYR 0.030 0.001 TYR C 156 ARG 0.007 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8136 (tp40) cc_final: 0.7626 (tp40) REVERT: A 533 LEU cc_start: 0.9014 (mp) cc_final: 0.8800 (mm) REVERT: B 297 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8535 (ptp-170) REVERT: B 305 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7990 (tptt) REVERT: B 601 MET cc_start: 0.8073 (tmt) cc_final: 0.7713 (tmt) REVERT: E 36 ASN cc_start: 0.8563 (t0) cc_final: 0.8298 (t0) REVERT: E 87 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7685 (tm-30) outliers start: 32 outliers final: 21 residues processed: 218 average time/residue: 1.6216 time to fit residues: 395.7669 Evaluate side-chains 219 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.6980 chunk 245 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 238 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 22128 Z= 0.155 Angle : 0.487 17.501 29881 Z= 0.252 Chirality : 0.036 0.183 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.367 18.213 2922 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.95 % Allowed : 14.63 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.17), residues: 2641 helix: 2.69 (0.12), residues: 1884 sheet: -2.10 (0.86), residues: 32 loop : 0.15 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.012 0.001 PHE A 391 TYR 0.032 0.001 TYR C 156 ARG 0.006 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8079 (tp40) cc_final: 0.7630 (tp40) REVERT: A 533 LEU cc_start: 0.9013 (mp) cc_final: 0.8801 (mm) REVERT: B 305 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7882 (tptp) REVERT: E 36 ASN cc_start: 0.8526 (t0) cc_final: 0.8278 (t0) REVERT: E 87 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7666 (tm-30) outliers start: 23 outliers final: 11 residues processed: 209 average time/residue: 1.6314 time to fit residues: 382.2838 Evaluate side-chains 199 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 243 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.005 0.054 22128 Z= 0.332 Angle : 0.552 17.288 29881 Z= 0.284 Chirality : 0.040 0.189 3373 Planarity : 0.004 0.046 3811 Dihedral : 3.504 20.313 2922 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.78 % Allowed : 14.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.73 (0.17), residues: 2641 helix: 2.53 (0.12), residues: 1882 sheet: -2.24 (0.87), residues: 32 loop : 0.09 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 845 HIS 0.006 0.001 HIS A1128 PHE 0.018 0.002 PHE B1002 TYR 0.031 0.001 TYR C 156 ARG 0.007 0.000 ARG B 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8126 (tp40) cc_final: 0.7621 (tp40) REVERT: A 533 LEU cc_start: 0.9016 (mp) cc_final: 0.8802 (mm) REVERT: B 297 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8440 (ptp-170) REVERT: B 305 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (tptt) REVERT: B 601 MET cc_start: 0.8120 (tmt) cc_final: 0.7856 (tmt) REVERT: E 36 ASN cc_start: 0.8542 (t0) cc_final: 0.8271 (t0) REVERT: E 87 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7658 (tm-30) outliers start: 19 outliers final: 13 residues processed: 204 average time/residue: 1.6939 time to fit residues: 385.7495 Evaluate side-chains 208 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069777 restraints weight = 45354.617| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.80 r_work: 0.2989 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22128 Z= 0.197 Angle : 0.503 17.149 29881 Z= 0.259 Chirality : 0.037 0.186 3373 Planarity : 0.003 0.047 3811 Dihedral : 3.432 18.989 2922 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.66 % Allowed : 15.12 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.86 (0.17), residues: 2641 helix: 2.63 (0.12), residues: 1880 sheet: -2.12 (0.87), residues: 32 loop : 0.12 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.013 0.001 PHE A 391 TYR 0.032 0.001 TYR C 156 ARG 0.007 0.000 ARG E 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7555.77 seconds wall clock time: 134 minutes 27.52 seconds (8067.52 seconds total)