Starting phenix.real_space_refine on Sat Mar 16 07:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8z_30615/03_2024/7d8z_30615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8z_30615/03_2024/7d8z_30615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8z_30615/03_2024/7d8z_30615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8z_30615/03_2024/7d8z_30615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8z_30615/03_2024/7d8z_30615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8z_30615/03_2024/7d8z_30615.pdb" } resolution = 3.4 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= 0.003 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 114 5.16 5 C 9006 2.51 5 N 2370 2.21 5 O 2508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 531": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 677": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 869": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 1078": "NH1" <-> "NH2" Residue "B ARG 1088": "NH1" <-> "NH2" Residue "B ARG 1102": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 677": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 869": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 1078": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1102": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6943 Classifications: {'peptide': 895} Link IDs: {'PTRANS': 34, 'TRANS': 860} Chain breaks: 2 Chain: "A" Number of atoms: 6943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6943 Classifications: {'peptide': 895} Link IDs: {'PTRANS': 34, 'TRANS': 860} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.13, per 1000 atoms: 0.51 Number of scatterers: 13998 At special positions: 0 Unit cell: (114.582, 124.722, 153.114, 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 114 16.00 O 2508 8.00 N 2370 7.00 C 9006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 629 " distance=2.01 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 629 " distance=2.01 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 354 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1201 " - " ASN A 362 " " NAG A1202 " - " ASN A 351 " " NAG B1201 " - " ASN B 362 " " NAG B1202 " - " ASN B 351 " " NAG C 1 " - " ASN B 314 " " NAG D 1 " - " ASN A 314 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.5 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 6 sheets defined 59.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.777A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.627A pdb=" N ILE B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 179 removed outlier: 3.621A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 161 " --> pdb=" O CYS B 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 229 removed outlier: 3.581A pdb=" N SER B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Proline residue: B 197 - end of helix removed outlier: 3.798A pdb=" N GLY B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 271 removed outlier: 3.682A pdb=" N MET B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.671A pdb=" N LYS B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 303 removed outlier: 3.608A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.681A pdb=" N PHE B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.501A pdb=" N ASN B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.840A pdb=" N LEU B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.870A pdb=" N SER B 441 " --> pdb=" O MET B 438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 478 removed outlier: 3.811A pdb=" N ILE B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.591A pdb=" N THR B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 487 through 494 removed outlier: 4.010A pdb=" N GLY B 490 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 491 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA B 492 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 507 through 525 removed outlier: 3.726A pdb=" N VAL B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 540 removed outlier: 3.564A pdb=" N ARG B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 550 removed outlier: 3.525A pdb=" N LEU B 545 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 547 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 550 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 4.022A pdb=" N ILE B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 605 removed outlier: 3.526A pdb=" N ALA B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Proline residue: B 582 - end of helix removed outlier: 3.775A pdb=" N PHE B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 603 " --> pdb=" O CYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 637 removed outlier: 3.752A pdb=" N GLY B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET B 633 " --> pdb=" O CYS B 629 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 637 " --> pdb=" O MET B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 664 removed outlier: 4.554A pdb=" N VAL B 643 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 661 " --> pdb=" O TYR B 657 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 662 " --> pdb=" O ARG B 658 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 663 " --> pdb=" O GLY B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 683 removed outlier: 3.677A pdb=" N ALA B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 4.116A pdb=" N LEU B 715 " --> pdb=" O HIS B 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 740 Processing helix chain 'B' and resid 741 through 759 removed outlier: 3.933A pdb=" N ILE B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 779 removed outlier: 3.518A pdb=" N GLY B 776 " --> pdb=" O ASN B 772 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 825 removed outlier: 3.530A pdb=" N PHE B 814 " --> pdb=" O THR B 810 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 815 " --> pdb=" O TRP B 811 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 862 Processing helix chain 'B' and resid 862 through 870 removed outlier: 4.087A pdb=" N PHE B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS B 870 " --> pdb=" O PHE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 905 removed outlier: 3.828A pdb=" N THR B 899 " --> pdb=" O LYS B 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 901 " --> pdb=" O ASP B 897 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 903 " --> pdb=" O THR B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1085 removed outlier: 3.672A pdb=" N THR B1075 " --> pdb=" O ARG B1071 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B1077 " --> pdb=" O MET B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1118 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.777A pdb=" N ALA A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.627A pdb=" N ILE A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 179 removed outlier: 3.621A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 229 removed outlier: 3.581A pdb=" N SER A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.798A pdb=" N GLY A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 271 removed outlier: 3.682A pdb=" N MET A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.671A pdb=" N LYS A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 303 removed outlier: 3.608A pdb=" N PHE A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.681A pdb=" N PHE A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.501A pdb=" N ASN A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.840A pdb=" N LEU A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.870A pdb=" N SER A 441 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 478 removed outlier: 3.811A pdb=" N ILE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 3.591A pdb=" N THR A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 487 through 494 removed outlier: 4.010A pdb=" N GLY A 490 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 491 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.726A pdb=" N VAL A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 removed outlier: 3.564A pdb=" N ARG A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 removed outlier: 3.525A pdb=" N LEU A 545 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 550 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 4.022A pdb=" N ILE A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 605 removed outlier: 3.526A pdb=" N ALA A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 3.775A pdb=" N PHE A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 603 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.752A pdb=" N GLY A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 633 " --> pdb=" O CYS A 629 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 637 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 664 removed outlier: 4.554A pdb=" N VAL A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 661 " --> pdb=" O TYR A 657 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 removed outlier: 3.677A pdb=" N ALA A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 removed outlier: 4.116A pdb=" N LEU A 715 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'A' and resid 741 through 759 removed outlier: 3.933A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 779 removed outlier: 3.518A pdb=" N GLY A 776 " --> pdb=" O ASN A 772 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 825 removed outlier: 3.530A pdb=" N PHE A 814 " --> pdb=" O THR A 810 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 862 through 870 removed outlier: 4.087A pdb=" N PHE A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 870 " --> pdb=" O PHE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 905 removed outlier: 3.828A pdb=" N THR A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1085 removed outlier: 3.672A pdb=" N THR A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A1077 " --> pdb=" O MET A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1118 Processing sheet with id=AA1, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AA2, first strand: chain 'B' and resid 328 through 331 Processing sheet with id=AA3, first strand: chain 'B' and resid 764 through 770 removed outlier: 6.552A pdb=" N VAL B 730 " --> pdb=" O GLN B 766 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 768 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER B 732 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER B 770 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU B 734 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 697 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY B 731 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 699 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL B 733 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 701 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N GLU B 735 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 698 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B1124 " --> pdb=" O LYS B 832 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B1093 " --> pdb=" O MET B1125 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B1127 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B1095 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLY B1129 " --> pdb=" O LEU B1095 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 848 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU B1094 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 850 " --> pdb=" O LEU B1094 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ASN B1096 " --> pdb=" O ASP B 850 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP B 852 " --> pdb=" O ASN B1096 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 331 Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 770 removed outlier: 6.552A pdb=" N VAL A 730 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 768 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 732 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER A 770 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A 734 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 697 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY A 731 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 699 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL A 733 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL A 701 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N GLU A 735 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 698 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A1124 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A1093 " --> pdb=" O MET A1125 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A1127 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A1095 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLY A1129 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 848 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU A1094 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP A 850 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ASN A1096 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP A 852 " --> pdb=" O ASN A1096 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1809 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: 4.02 Time building geometry restraints manager: 5.79 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: 4448 1.34 - 1.47: 3534 1.47 - 1.59: 6144 1.59 - 1.71: 0 1.71 - 1.84: 182 Bond restraints: 14308 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA THR B 435 " pdb=" CB THR B 435 " ideal model delta sigma weight residual 1.532 1.492 0.039 1.74e-02 3.30e+03 5.05e+00 bond pdb=" CA THR A 435 " pdb=" CB THR A 435 " ideal model delta sigma weight residual 1.532 1.492 0.039 1.74e-02 3.30e+03 5.05e+00 bond pdb=" CA ASP B 807 " pdb=" C ASP B 807 " ideal model delta sigma weight residual 1.523 1.552 -0.029 1.34e-02 5.57e+03 4.75e+00 ... (remaining 14303 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.22: 236 104.22 - 111.67: 6592 111.67 - 119.12: 5052 119.12 - 126.58: 7290 126.58 - 134.03: 244 Bond angle restraints: 19414 Sorted by residual: angle pdb=" N GLN B 707 " pdb=" CA GLN B 707 " pdb=" C GLN B 707 " ideal model delta sigma weight residual 110.24 122.73 -12.49 1.47e+00 4.63e-01 7.22e+01 angle pdb=" N GLN A 707 " pdb=" CA GLN A 707 " pdb=" C GLN A 707 " ideal model delta sigma weight residual 110.24 122.73 -12.49 1.47e+00 4.63e-01 7.22e+01 angle pdb=" N ASP A 706 " pdb=" CA ASP A 706 " pdb=" C ASP A 706 " ideal model delta sigma weight residual 111.24 99.95 11.29 1.38e+00 5.25e-01 6.70e+01 angle pdb=" N ASP B 706 " pdb=" CA ASP B 706 " pdb=" C ASP B 706 " ideal model delta sigma weight residual 111.24 99.95 11.29 1.38e+00 5.25e-01 6.70e+01 angle pdb=" N VAL A 181 " pdb=" CA VAL A 181 " pdb=" C VAL A 181 " ideal model delta sigma weight residual 112.43 106.76 5.67 9.20e-01 1.18e+00 3.80e+01 ... (remaining 19409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 8040 15.43 - 30.86: 382 30.86 - 46.29: 98 46.29 - 61.73: 14 61.73 - 77.16: 8 Dihedral angle restraints: 8542 sinusoidal: 3444 harmonic: 5098 Sorted by residual: dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 629 " pdb=" CB CYS B 629 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 629 " pdb=" CB CYS A 629 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 206 " pdb=" SG CYS A 206 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 153.65 -60.65 1 1.00e+01 1.00e-02 4.89e+01 ... (remaining 8539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2094 0.109 - 0.218: 140 0.218 - 0.327: 10 0.327 - 0.436: 2 0.436 - 0.545: 2 Chirality restraints: 2248 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 314 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 314 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA GLN A 707 " pdb=" N GLN A 707 " pdb=" C GLN A 707 " pdb=" CB GLN A 707 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 2245 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 129 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 129 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 506 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 507 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.031 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2262 2.75 - 3.29: 13336 3.29 - 3.82: 22103 3.82 - 4.36: 26367 4.36 - 4.90: 44572 Nonbonded interactions: 108640 Sorted by model distance: nonbonded pdb=" O GLN A 707 " pdb=" OD1 ASN A 708 " model vdw 2.209 3.040 nonbonded pdb=" O GLN B 707 " pdb=" OD1 ASN B 708 " model vdw 2.209 3.040 nonbonded pdb=" O HIS A 779 " pdb=" OG SER A 783 " model vdw 2.240 2.440 nonbonded pdb=" O HIS B 779 " pdb=" OG SER B 783 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR B 607 " pdb=" OH TYR B 678 " model vdw 2.255 2.440 ... (remaining 108635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 36.770 Find NCS groups from input model: 0.680 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.009 0.079 14308 Z= 0.549 Angle : 1.148 12.489 19414 Z= 0.651 Chirality : 0.062 0.545 2248 Planarity : 0.007 0.055 2430 Dihedral : 10.330 77.158 5258 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.22 % Favored : 90.66 % Rotamer: Outliers : 0.53 % Allowed : 3.60 % Favored : 95.87 % 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: -5.56 (0.13), residues: 1778 helix: -4.09 (0.09), residues: 926 sheet: -0.92 (0.36), residues: 168 loop : -3.60 (0.17), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 382 HIS 0.016 0.003 HIS A 808 PHE 0.032 0.003 PHE B 416 TYR 0.023 0.003 TYR A 189 ARG 0.011 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 367 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 353 THR cc_start: 0.6861 (p) cc_final: 0.6584 (t) REVERT: B 524 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 727 LEU cc_start: 0.8646 (tp) cc_final: 0.8274 (tp) REVERT: B 760 LYS cc_start: 0.7937 (mptt) cc_final: 0.7691 (mmmt) REVERT: B 836 MET cc_start: 0.8070 (ptm) cc_final: 0.7822 (ptm) REVERT: A 353 THR cc_start: 0.6855 (p) cc_final: 0.6585 (t) REVERT: A 524 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 727 LEU cc_start: 0.8656 (tp) cc_final: 0.8285 (tp) REVERT: A 760 LYS cc_start: 0.7935 (mptt) cc_final: 0.7691 (mmmt) REVERT: A 836 MET cc_start: 0.8064 (ptm) cc_final: 0.7810 (ptm) outliers start: 8 outliers final: 2 residues processed: 373 average time/residue: 0.3221 time to fit residues: 162.3118 Evaluate side-chains 211 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 103 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 HIS ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN B 808 HIS B 871 HIS B1096 ASN A 361 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS A 871 HIS A1096 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14308 Z= 0.207 Angle : 0.724 9.450 19414 Z= 0.372 Chirality : 0.045 0.254 2248 Planarity : 0.005 0.046 2430 Dihedral : 7.302 53.868 2104 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.67 % Allowed : 10.67 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.16), residues: 1778 helix: -2.18 (0.13), residues: 970 sheet: -0.66 (0.38), residues: 168 loop : -3.27 (0.19), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 693 HIS 0.010 0.002 HIS A1074 PHE 0.021 0.002 PHE B 156 TYR 0.029 0.002 TYR B 414 ARG 0.006 0.001 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 264 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7729 (t80) cc_final: 0.7508 (t80) REVERT: B 800 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7275 (tpp80) REVERT: B 879 MET cc_start: 0.7585 (ttm) cc_final: 0.7356 (ttm) REVERT: A 160 PHE cc_start: 0.7732 (t80) cc_final: 0.7507 (t80) REVERT: A 800 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7258 (tpp80) REVERT: A 879 MET cc_start: 0.7624 (ttm) cc_final: 0.7378 (ttm) outliers start: 25 outliers final: 15 residues processed: 279 average time/residue: 0.2480 time to fit residues: 101.7925 Evaluate side-chains 207 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 174 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A1096 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14308 Z= 0.180 Angle : 0.636 7.656 19414 Z= 0.322 Chirality : 0.043 0.211 2248 Planarity : 0.004 0.037 2430 Dihedral : 6.456 45.546 2104 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.67 % Allowed : 11.80 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.66 (0.18), residues: 1778 helix: -1.13 (0.16), residues: 970 sheet: -0.59 (0.37), residues: 168 loop : -3.01 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 693 HIS 0.003 0.001 HIS A 904 PHE 0.024 0.001 PHE B 207 TYR 0.012 0.001 TYR A 430 ARG 0.010 0.001 ARG A 880 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7762 (t80) cc_final: 0.7533 (t80) REVERT: B 578 ASP cc_start: 0.6739 (p0) cc_final: 0.6524 (p0) REVERT: B 583 ILE cc_start: 0.8582 (mt) cc_final: 0.8318 (mt) REVERT: B 800 ARG cc_start: 0.7950 (mmm160) cc_final: 0.7325 (ttm170) REVERT: B 863 LEU cc_start: 0.8760 (tp) cc_final: 0.8392 (tp) REVERT: B 907 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.4726 (mp) REVERT: A 160 PHE cc_start: 0.7762 (t80) cc_final: 0.7533 (t80) REVERT: A 583 ILE cc_start: 0.8581 (mt) cc_final: 0.8316 (mt) REVERT: A 789 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7646 (pp) REVERT: A 800 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7335 (ttm170) REVERT: A 863 LEU cc_start: 0.8758 (tp) cc_final: 0.8386 (tp) REVERT: A 907 ILE cc_start: 0.5106 (OUTLIER) cc_final: 0.4751 (mp) outliers start: 40 outliers final: 24 residues processed: 256 average time/residue: 0.2436 time to fit residues: 92.8848 Evaluate side-chains 223 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 84 optimal weight: 0.0050 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN B1074 HIS ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14308 Z= 0.198 Angle : 0.623 7.816 19414 Z= 0.314 Chirality : 0.043 0.183 2248 Planarity : 0.003 0.028 2430 Dihedral : 5.973 53.027 2104 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.60 % Allowed : 11.87 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.18 (0.18), residues: 1778 helix: -0.68 (0.16), residues: 972 sheet: -0.50 (0.37), residues: 168 loop : -2.85 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 693 HIS 0.011 0.001 HIS A1074 PHE 0.027 0.002 PHE A 207 TYR 0.007 0.001 TYR A 430 ARG 0.005 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7816 (t80) cc_final: 0.7591 (t80) REVERT: B 583 ILE cc_start: 0.8601 (mt) cc_final: 0.8360 (mt) REVERT: B 721 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8428 (tt) REVERT: B 789 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7662 (pp) REVERT: B 863 LEU cc_start: 0.8801 (tp) cc_final: 0.8398 (tp) REVERT: B 864 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8583 (mm) REVERT: B 907 ILE cc_start: 0.5195 (OUTLIER) cc_final: 0.4872 (mp) REVERT: A 160 PHE cc_start: 0.7814 (t80) cc_final: 0.7588 (t80) REVERT: A 583 ILE cc_start: 0.8596 (mt) cc_final: 0.8353 (mt) REVERT: A 721 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 789 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7669 (pp) REVERT: A 863 LEU cc_start: 0.8768 (tp) cc_final: 0.8362 (tp) REVERT: A 864 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 907 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4882 (mp) outliers start: 69 outliers final: 43 residues processed: 258 average time/residue: 0.2327 time to fit residues: 91.1500 Evaluate side-chains 254 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.0170 chunk 146 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A1074 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14308 Z= 0.208 Angle : 0.615 7.345 19414 Z= 0.310 Chirality : 0.043 0.179 2248 Planarity : 0.003 0.032 2430 Dihedral : 5.778 43.345 2104 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.87 % Allowed : 13.47 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.83 (0.19), residues: 1778 helix: -0.31 (0.16), residues: 958 sheet: -0.36 (0.37), residues: 168 loop : -2.80 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 811 HIS 0.003 0.001 HIS A1074 PHE 0.027 0.002 PHE A 207 TYR 0.010 0.001 TYR A 294 ARG 0.005 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 207 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7831 (t80) cc_final: 0.7604 (t80) REVERT: B 410 MET cc_start: 0.8212 (ppp) cc_final: 0.8007 (ppp) REVERT: B 583 ILE cc_start: 0.8565 (mt) cc_final: 0.8338 (mt) REVERT: B 721 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8547 (tt) REVERT: B 789 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7771 (pp) REVERT: B 863 LEU cc_start: 0.8777 (tp) cc_final: 0.8397 (tp) REVERT: B 907 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4755 (mp) REVERT: A 160 PHE cc_start: 0.7829 (t80) cc_final: 0.7600 (t80) REVERT: A 410 MET cc_start: 0.8207 (ppp) cc_final: 0.7999 (ppp) REVERT: A 583 ILE cc_start: 0.8558 (mt) cc_final: 0.8330 (mt) REVERT: A 721 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 789 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7634 (pp) REVERT: A 863 LEU cc_start: 0.8804 (tp) cc_final: 0.8406 (tp) REVERT: A 907 ILE cc_start: 0.5131 (OUTLIER) cc_final: 0.4760 (mp) outliers start: 73 outliers final: 51 residues processed: 256 average time/residue: 0.2426 time to fit residues: 92.6424 Evaluate side-chains 248 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 191 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 HIS B1096 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14308 Z= 0.216 Angle : 0.630 9.433 19414 Z= 0.314 Chirality : 0.043 0.234 2248 Planarity : 0.003 0.026 2430 Dihedral : 5.753 51.204 2104 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.67 % Allowed : 13.93 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.19), residues: 1778 helix: -0.07 (0.17), residues: 964 sheet: -0.28 (0.38), residues: 168 loop : -2.78 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 341 HIS 0.008 0.001 HIS A1074 PHE 0.029 0.002 PHE B 207 TYR 0.009 0.001 TYR A 617 ARG 0.006 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 198 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7848 (t80) cc_final: 0.7630 (t80) REVERT: B 410 MET cc_start: 0.8112 (ppp) cc_final: 0.7889 (ppp) REVERT: B 789 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7856 (pp) REVERT: B 863 LEU cc_start: 0.8697 (tp) cc_final: 0.8336 (tp) REVERT: B 907 ILE cc_start: 0.5267 (OUTLIER) cc_final: 0.4899 (mp) REVERT: A 160 PHE cc_start: 0.7845 (t80) cc_final: 0.7627 (t80) REVERT: A 410 MET cc_start: 0.8103 (ppp) cc_final: 0.7885 (ppp) REVERT: A 583 ILE cc_start: 0.8552 (mt) cc_final: 0.8331 (mt) REVERT: A 789 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7682 (pp) REVERT: A 863 LEU cc_start: 0.8719 (tp) cc_final: 0.8341 (tp) REVERT: A 907 ILE cc_start: 0.5206 (OUTLIER) cc_final: 0.4828 (mp) outliers start: 70 outliers final: 47 residues processed: 248 average time/residue: 0.2394 time to fit residues: 88.8847 Evaluate side-chains 244 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 193 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN B 442 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14308 Z= 0.301 Angle : 0.690 10.974 19414 Z= 0.343 Chirality : 0.045 0.201 2248 Planarity : 0.004 0.042 2430 Dihedral : 5.842 43.089 2104 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.60 % Allowed : 14.60 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.59 (0.19), residues: 1778 helix: -0.08 (0.17), residues: 978 sheet: -0.16 (0.39), residues: 166 loop : -2.87 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 341 HIS 0.006 0.001 HIS A1074 PHE 0.028 0.002 PHE B 207 TYR 0.011 0.002 TYR A 617 ARG 0.007 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 191 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7876 (t80) cc_final: 0.7631 (t80) REVERT: B 410 MET cc_start: 0.8083 (ppp) cc_final: 0.7820 (ppp) REVERT: B 626 MET cc_start: 0.8188 (tpp) cc_final: 0.7873 (tpp) REVERT: B 775 ASP cc_start: 0.8346 (m-30) cc_final: 0.8143 (m-30) REVERT: B 863 LEU cc_start: 0.8713 (tp) cc_final: 0.8329 (tp) REVERT: B 872 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8605 (ptmt) REVERT: B 907 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.4931 (mp) REVERT: A 160 PHE cc_start: 0.7873 (t80) cc_final: 0.7628 (t80) REVERT: A 410 MET cc_start: 0.8079 (ppp) cc_final: 0.7819 (ppp) REVERT: A 626 MET cc_start: 0.8187 (tpp) cc_final: 0.7878 (tpp) REVERT: A 789 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7759 (pp) REVERT: A 863 LEU cc_start: 0.8724 (tp) cc_final: 0.8320 (tp) REVERT: A 907 ILE cc_start: 0.5343 (OUTLIER) cc_final: 0.4936 (mp) outliers start: 69 outliers final: 51 residues processed: 248 average time/residue: 0.2250 time to fit residues: 85.5004 Evaluate side-chains 237 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 182 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14308 Z= 0.303 Angle : 0.731 12.839 19414 Z= 0.359 Chirality : 0.046 0.264 2248 Planarity : 0.004 0.038 2430 Dihedral : 6.043 51.252 2104 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 5.00 % Allowed : 15.20 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1778 helix: -0.12 (0.17), residues: 978 sheet: -0.13 (0.39), residues: 166 loop : -2.87 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 811 HIS 0.006 0.001 HIS A1074 PHE 0.025 0.002 PHE B 207 TYR 0.010 0.001 TYR B 617 ARG 0.006 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 184 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7827 (t80) cc_final: 0.7571 (t80) REVERT: B 410 MET cc_start: 0.8103 (ppp) cc_final: 0.7826 (ppp) REVERT: B 594 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: B 626 MET cc_start: 0.8116 (tpp) cc_final: 0.7790 (tpp) REVERT: B 789 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (pp) REVERT: B 862 MET cc_start: 0.7989 (mpp) cc_final: 0.7618 (mpp) REVERT: B 863 LEU cc_start: 0.8655 (tp) cc_final: 0.8239 (tp) REVERT: B 872 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8648 (ptmt) REVERT: B 907 ILE cc_start: 0.5318 (OUTLIER) cc_final: 0.4944 (mp) REVERT: A 160 PHE cc_start: 0.7855 (t80) cc_final: 0.7598 (t80) REVERT: A 410 MET cc_start: 0.8100 (ppp) cc_final: 0.7824 (ppp) REVERT: A 594 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: A 626 MET cc_start: 0.8108 (tpp) cc_final: 0.7782 (tpp) REVERT: A 789 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7879 (pp) REVERT: A 863 LEU cc_start: 0.8700 (tp) cc_final: 0.8246 (tp) REVERT: A 907 ILE cc_start: 0.5369 (OUTLIER) cc_final: 0.4970 (mp) outliers start: 75 outliers final: 62 residues processed: 244 average time/residue: 0.2459 time to fit residues: 90.7989 Evaluate side-chains 246 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 177 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 914 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 0.0370 chunk 169 optimal weight: 5.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14308 Z= 0.171 Angle : 0.665 10.856 19414 Z= 0.325 Chirality : 0.043 0.187 2248 Planarity : 0.003 0.032 2430 Dihedral : 5.757 47.281 2104 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.60 % Allowed : 17.20 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.48 (0.19), residues: 1778 helix: 0.01 (0.17), residues: 974 sheet: 0.03 (0.40), residues: 166 loop : -2.84 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 811 HIS 0.007 0.001 HIS A1074 PHE 0.028 0.001 PHE B 207 TYR 0.008 0.001 TYR A 430 ARG 0.012 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 199 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7828 (t80) cc_final: 0.7586 (t80) REVERT: B 410 MET cc_start: 0.8094 (ppp) cc_final: 0.7744 (ppp) REVERT: B 594 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 626 MET cc_start: 0.7934 (tpp) cc_final: 0.7701 (tpp) REVERT: B 789 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8026 (pp) REVERT: B 800 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7428 (ttm170) REVERT: B 863 LEU cc_start: 0.8583 (tp) cc_final: 0.8239 (tp) REVERT: B 907 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.5122 (mp) REVERT: A 160 PHE cc_start: 0.7827 (t80) cc_final: 0.7588 (t80) REVERT: A 410 MET cc_start: 0.8087 (ppp) cc_final: 0.7745 (ppp) REVERT: A 594 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: A 626 MET cc_start: 0.7950 (tpp) cc_final: 0.7703 (tpp) REVERT: A 789 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 800 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7384 (ttm170) REVERT: A 863 LEU cc_start: 0.8601 (tp) cc_final: 0.8245 (tp) REVERT: A 907 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.5298 (mp) REVERT: A 1125 MET cc_start: 0.8111 (ttm) cc_final: 0.7817 (tpp) outliers start: 54 outliers final: 34 residues processed: 242 average time/residue: 0.2324 time to fit residues: 85.0815 Evaluate side-chains 224 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 14 optimal weight: 0.0270 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14308 Z= 0.212 Angle : 0.702 13.273 19414 Z= 0.339 Chirality : 0.044 0.192 2248 Planarity : 0.003 0.044 2430 Dihedral : 5.665 44.503 2104 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.00 % Allowed : 18.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.48 (0.19), residues: 1778 helix: 0.01 (0.17), residues: 968 sheet: 0.03 (0.39), residues: 166 loop : -2.82 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 811 HIS 0.006 0.001 HIS A1074 PHE 0.027 0.001 PHE B 207 TYR 0.008 0.001 TYR A 617 ARG 0.011 0.001 ARG A 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7856 (t80) cc_final: 0.7631 (t80) REVERT: B 410 MET cc_start: 0.8119 (ppp) cc_final: 0.7764 (ppp) REVERT: B 594 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: B 626 MET cc_start: 0.7959 (tpp) cc_final: 0.7678 (tpp) REVERT: B 789 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8086 (pp) REVERT: B 800 ARG cc_start: 0.7950 (mmm160) cc_final: 0.7406 (ttm170) REVERT: B 863 LEU cc_start: 0.8503 (tp) cc_final: 0.8277 (tp) REVERT: B 907 ILE cc_start: 0.5434 (OUTLIER) cc_final: 0.5203 (mp) REVERT: B 1125 MET cc_start: 0.8194 (ttm) cc_final: 0.7840 (tpp) REVERT: A 160 PHE cc_start: 0.7856 (t80) cc_final: 0.7628 (t80) REVERT: A 410 MET cc_start: 0.8114 (ppp) cc_final: 0.7761 (ppp) REVERT: A 578 ASP cc_start: 0.6766 (p0) cc_final: 0.6553 (p0) REVERT: A 594 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: A 789 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8007 (pp) REVERT: A 800 ARG cc_start: 0.7958 (mmm160) cc_final: 0.7393 (ttm170) REVERT: A 863 LEU cc_start: 0.8492 (tp) cc_final: 0.8253 (tp) REVERT: A 907 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.5147 (mp) REVERT: A 1125 MET cc_start: 0.8137 (ttm) cc_final: 0.7820 (tpp) outliers start: 45 outliers final: 36 residues processed: 228 average time/residue: 0.2348 time to fit residues: 81.6581 Evaluate side-chains 221 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 0.0370 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 0.1980 chunk 59 optimal weight: 0.1980 chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN ** A1074 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.120309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099364 restraints weight = 32184.255| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.96 r_work: 0.3444 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14308 Z= 0.168 Angle : 0.666 14.229 19414 Z= 0.322 Chirality : 0.043 0.177 2248 Planarity : 0.003 0.039 2430 Dihedral : 5.458 37.534 2104 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.07 % Allowed : 18.13 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1778 helix: 0.06 (0.17), residues: 982 sheet: 0.04 (0.40), residues: 166 loop : -2.76 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 811 HIS 0.006 0.001 HIS A1074 PHE 0.030 0.001 PHE B 207 TYR 0.007 0.001 TYR B 430 ARG 0.012 0.000 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.41 seconds wall clock time: 55 minutes 51.79 seconds (3351.79 seconds total)