Starting phenix.real_space_refine on Sat Mar 16 13:54:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1y_30049/03_2024/6m1y_30049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1y_30049/03_2024/6m1y_30049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1y_30049/03_2024/6m1y_30049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1y_30049/03_2024/6m1y_30049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1y_30049/03_2024/6m1y_30049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1y_30049/03_2024/6m1y_30049_updated.pdb" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 9594 2.51 5 N 2472 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A ARG 970": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 688": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B ARG 891": "NH1" <-> "NH2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B GLU 926": "OE1" <-> "OE2" Residue "B GLU 938": "OE1" <-> "OE2" Residue "B ARG 954": "NH1" <-> "NH2" Residue "B ARG 970": "NH1" <-> "NH2" Residue "B ARG 1031": "NH1" <-> "NH2" Residue "B ARG 1062": "NH1" <-> "NH2" Residue "B GLU 1068": "OE1" <-> "OE2" Residue "B ARG 1088": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14858 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7313 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 32, 'TRANS': 905} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7313 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 32, 'TRANS': 905} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 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: "E" 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: "F" 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: "G" 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: "H" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' K': 1, ' CL': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' K': 1, ' CL': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.83, per 1000 atoms: 0.53 Number of scatterers: 14858 At special positions: 0 Unit cell: (95.656, 116.309, 156.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 108 16.00 P 4 15.00 O 2674 8.00 N 2472 7.00 C 9594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.02 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.02 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1110 " - " ASN A 347 " " NAG A1111 " - " ASN A 360 " " NAG B1110 " - " ASN B 347 " " NAG B1111 " - " ASN B 360 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 377 " " NAG F 1 " - " ASN B 328 " " NAG G 1 " - " ASN B 366 " " NAG H 1 " - " ASN B 377 " Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.7 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 6 sheets defined 46.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 165 through 191 removed outlier: 4.106A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 180 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 removed outlier: 3.684A pdb=" N ARG A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 241 removed outlier: 3.537A pdb=" N ILE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 315 removed outlier: 3.725A pdb=" N ASN A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.758A pdb=" N PHE A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.595A pdb=" N VAL A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 448 through 451 removed outlier: 3.593A pdb=" N GLY A 451 " --> pdb=" O ILE A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 465 through 488 removed outlier: 3.637A pdb=" N LEU A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.535A pdb=" N ILE A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 522 " --> pdb=" O TRP A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 522' Processing helix chain 'A' and resid 524 through 548 removed outlier: 3.664A pdb=" N THR A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Proline residue: A 541 - end of helix removed outlier: 3.695A pdb=" N ALA A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 570 through 578 removed outlier: 3.698A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 588 through 613 Proline residue: A 593 - end of helix removed outlier: 3.648A pdb=" N MET A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 removed outlier: 3.676A pdb=" N ILE A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.782A pdb=" N ILE A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 660 " --> pdb=" O MET A 656 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.911A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 733 Processing helix chain 'A' and resid 753 through 769 removed outlier: 3.625A pdb=" N LEU A 757 " --> pdb=" O TYR A 753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 793 removed outlier: 3.821A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 834 removed outlier: 4.191A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 871 through 880 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 902 through 914 removed outlier: 3.510A pdb=" N THR A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 936 No H-bonds generated for 'chain 'A' and resid 933 through 936' Processing helix chain 'A' and resid 943 through 950 removed outlier: 3.509A pdb=" N MET A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 1037 through 1043 removed outlier: 3.977A pdb=" N GLU A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1077 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 165 through 191 removed outlier: 4.106A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 191 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.684A pdb=" N ARG B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.537A pdb=" N ILE B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 315 removed outlier: 3.725A pdb=" N ASN B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 303 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.758A pdb=" N PHE B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 374 No H-bonds generated for 'chain 'B' and resid 371 through 374' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.595A pdb=" N VAL B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 448 through 451 removed outlier: 3.593A pdb=" N GLY B 451 " --> pdb=" O ILE B 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 451' Processing helix chain 'B' and resid 465 through 488 removed outlier: 3.637A pdb=" N LEU B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 496 No H-bonds generated for 'chain 'B' and resid 493 through 496' Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.535A pdb=" N ILE B 521 " --> pdb=" O PRO B 518 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 522 " --> pdb=" O TRP B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 518 through 522' Processing helix chain 'B' and resid 524 through 548 removed outlier: 3.664A pdb=" N THR B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Proline residue: B 541 - end of helix removed outlier: 3.695A pdb=" N ALA B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.698A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 588 through 613 Proline residue: B 593 - end of helix removed outlier: 3.648A pdb=" N MET B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 605 " --> pdb=" O MET B 601 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 removed outlier: 3.676A pdb=" N ILE B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 675 removed outlier: 3.782A pdb=" N ILE B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 660 " --> pdb=" O MET B 656 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 673 " --> pdb=" O GLN B 669 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.911A pdb=" N SER B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 733 Processing helix chain 'B' and resid 753 through 769 removed outlier: 3.625A pdb=" N LEU B 757 " --> pdb=" O TYR B 753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 762 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 793 removed outlier: 3.821A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 834 removed outlier: 4.191A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 847 No H-bonds generated for 'chain 'B' and resid 845 through 847' Processing helix chain 'B' and resid 871 through 880 Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 902 through 914 removed outlier: 3.510A pdb=" N THR B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 936 No H-bonds generated for 'chain 'B' and resid 933 through 936' Processing helix chain 'B' and resid 943 through 950 removed outlier: 3.509A pdb=" N MET B 949 " --> pdb=" O GLN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 1037 through 1043 removed outlier: 3.977A pdb=" N GLU B1041 " --> pdb=" O VAL B1037 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B1042 " --> pdb=" O LYS B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1077 Processing sheet with id= A, first strand: chain 'A' and resid 322 through 325 Processing sheet with id= B, first strand: chain 'A' and resid 709 through 712 removed outlier: 6.816A pdb=" N ILE A 740 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU A 712 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 742 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE A 775 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N SER A 743 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN A 777 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE A 745 " --> pdb=" O GLN A 777 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 779 " --> pdb=" O ILE A 745 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 804 through 808 removed outlier: 6.515A pdb=" N ALA A 838 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N MET A 807 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 840 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N LEU A1054 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP A 861 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN A1056 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TRP A 863 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 322 through 325 Processing sheet with id= E, first strand: chain 'B' and resid 709 through 712 removed outlier: 6.816A pdb=" N ILE B 740 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU B 712 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 742 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE B 775 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N SER B 743 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN B 777 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE B 745 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 779 " --> pdb=" O ILE B 745 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 804 through 808 removed outlier: 6.515A pdb=" N ALA B 838 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N MET B 807 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 840 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N LEU B1054 " --> pdb=" O ASN B 859 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP B 861 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN B1056 " --> pdb=" O ASP B 861 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TRP B 863 " --> pdb=" O ASN B1056 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1404 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: 4.41 Time building geometry restraints manager: 5.94 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: 4614 1.34 - 1.46: 3246 1.46 - 1.58: 7126 1.58 - 1.69: 12 1.69 - 1.81: 178 Bond restraints: 15176 Sorted by residual: bond pdb=" OG1 TPO B 997 " pdb=" P TPO B 997 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO A 997 " pdb=" P TPO A 997 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO A 940 " pdb=" P TPO A 940 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" OG1 TPO B 940 " pdb=" P TPO B 940 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C GLY A 697 " pdb=" N PRO A 698 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.18e-02 7.18e+03 2.66e+01 ... (remaining 15171 not shown) Histogram of bond angle deviations from ideal: 99.60 - 107.39: 556 107.39 - 115.18: 9256 115.18 - 122.97: 9690 122.97 - 130.76: 980 130.76 - 138.55: 102 Bond angle restraints: 20584 Sorted by residual: angle pdb=" C GLY A 697 " pdb=" N PRO A 698 " pdb=" CA PRO A 698 " ideal model delta sigma weight residual 120.38 114.00 6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" C GLY B 697 " pdb=" N PRO B 698 " pdb=" CA PRO B 698 " ideal model delta sigma weight residual 120.38 114.00 6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" C ARG A 705 " pdb=" N PRO A 706 " pdb=" CA PRO A 706 " ideal model delta sigma weight residual 119.76 114.23 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C ARG B 705 " pdb=" N PRO B 706 " pdb=" CA PRO B 706 " ideal model delta sigma weight residual 119.76 114.23 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C ALA A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 ... (remaining 20579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 8152 17.08 - 34.15: 784 34.15 - 51.23: 174 51.23 - 68.30: 30 68.30 - 85.38: 18 Dihedral angle restraints: 9158 sinusoidal: 3768 harmonic: 5390 Sorted by residual: dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -166.84 80.84 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 324 " pdb=" SG CYS B 324 " pdb=" SG CYS B 339 " pdb=" CB CYS B 339 " ideal model delta sinusoidal sigma weight residual -86.00 -166.84 80.84 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CA LEU B 584 " pdb=" C LEU B 584 " pdb=" N ILE B 585 " pdb=" CA ILE B 585 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 9155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 2408 0.224 - 0.449: 10 0.449 - 0.673: 0 0.673 - 0.898: 0 0.898 - 1.122: 2 Chirality restraints: 2420 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 377 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2417 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 347 " 0.008 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" CG ASN B 347 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN B 347 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN B 347 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1110 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 347 " 0.008 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" CG ASN A 347 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN A 347 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN A 347 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG A1110 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 347 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" CG ASN A 347 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 347 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 347 " 0.020 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 4662 2.82 - 3.40: 14520 3.40 - 3.98: 25377 3.98 - 4.56: 36784 4.56 - 5.14: 53647 Nonbonded interactions: 134990 Sorted by model distance: nonbonded pdb=" O ARG A 951 " pdb=" N MET A 953 " model vdw 2.245 2.520 nonbonded pdb=" O ARG B 951 " pdb=" N MET B 953 " model vdw 2.245 2.520 nonbonded pdb=" O GLN A 707 " pdb=" O LEU A 738 " model vdw 2.248 3.040 nonbonded pdb=" O GLN B 707 " pdb=" O LEU B 738 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 308 " pdb=" OG SER B 482 " model vdw 2.256 2.440 ... (remaining 134985 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.580 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 39.880 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.110 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: 53.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.006 0.111 15176 Z= 0.386 Angle : 0.950 13.553 20584 Z= 0.497 Chirality : 0.064 1.122 2420 Planarity : 0.006 0.068 2540 Dihedral : 14.122 85.376 5678 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 1.41 % Allowed : 9.63 % Favored : 88.96 % Rotamer: Outliers : 1.65 % Allowed : 6.36 % Favored : 91.98 % 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: -6.04 (0.13), residues: 1848 helix: -4.94 (0.04), residues: 898 sheet: -0.94 (0.37), residues: 168 loop : -3.38 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.003 0.001 HIS A 252 PHE 0.022 0.002 PHE B 555 TYR 0.014 0.002 TYR B 243 ARG 0.007 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.7650 (tp) cc_final: 0.7340 (tp) REVERT: A 343 LYS cc_start: 0.9001 (tttp) cc_final: 0.8644 (tptp) REVERT: A 783 LYS cc_start: 0.8960 (mttt) cc_final: 0.8759 (mttp) REVERT: A 995 HIS cc_start: 0.7342 (t-90) cc_final: 0.7025 (t-170) REVERT: A 1071 MET cc_start: 0.9347 (mmm) cc_final: 0.9090 (tpp) REVERT: B 326 LEU cc_start: 0.7648 (tp) cc_final: 0.7340 (tp) REVERT: B 343 LYS cc_start: 0.9004 (tttp) cc_final: 0.8646 (tptp) REVERT: B 783 LYS cc_start: 0.8962 (mttt) cc_final: 0.8762 (mttp) REVERT: B 995 HIS cc_start: 0.7343 (t-90) cc_final: 0.7025 (t-170) REVERT: B 1071 MET cc_start: 0.9346 (mmm) cc_final: 0.9088 (tpp) outliers start: 26 outliers final: 6 residues processed: 296 average time/residue: 0.2899 time to fit residues: 122.2862 Evaluate side-chains 148 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 700 HIS Chi-restraints excluded: chain B residue 815 GLN Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.0060 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 607 ASN A 613 GLN A 700 HIS A 707 GLN A 882 HIS A 952 HIS A 965 GLN B 399 ASN B 507 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 613 GLN B 700 HIS B 707 GLN B 882 HIS B 952 HIS B 965 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15176 Z= 0.190 Angle : 0.663 11.632 20584 Z= 0.339 Chirality : 0.046 0.643 2420 Planarity : 0.005 0.048 2540 Dihedral : 7.115 58.950 2354 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.77 % Favored : 90.80 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.28 % 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: -4.24 (0.16), residues: 1848 helix: -2.89 (0.12), residues: 918 sheet: -0.84 (0.36), residues: 168 loop : -3.04 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 515 HIS 0.003 0.001 HIS A 700 PHE 0.012 0.001 PHE A 555 TYR 0.008 0.001 TYR A 650 ARG 0.008 0.001 ARG A1032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 SER cc_start: 0.8737 (m) cc_final: 0.8464 (p) REVERT: A 343 LYS cc_start: 0.8990 (tttp) cc_final: 0.8708 (tptp) REVERT: A 943 MET cc_start: 0.8295 (tmm) cc_final: 0.8055 (tmm) REVERT: B 315 SER cc_start: 0.8738 (m) cc_final: 0.8464 (p) REVERT: B 343 LYS cc_start: 0.8989 (tttp) cc_final: 0.8707 (tptp) REVERT: B 943 MET cc_start: 0.8295 (tmm) cc_final: 0.8057 (tmm) outliers start: 36 outliers final: 8 residues processed: 184 average time/residue: 0.2396 time to fit residues: 66.6399 Evaluate side-chains 126 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 700 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 169 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15176 Z= 0.212 Angle : 0.625 8.942 20584 Z= 0.311 Chirality : 0.047 0.612 2420 Planarity : 0.004 0.052 2540 Dihedral : 6.445 44.639 2346 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.98 % Favored : 90.69 % Rotamer: Outliers : 0.76 % Allowed : 14.12 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.18), residues: 1848 helix: -1.36 (0.16), residues: 920 sheet: -0.77 (0.37), residues: 168 loop : -2.84 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 515 HIS 0.010 0.001 HIS B 995 PHE 0.010 0.001 PHE A 555 TYR 0.012 0.001 TYR A 243 ARG 0.004 0.000 ARG B1032 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8195 (mmm) cc_final: 0.7800 (mmm) REVERT: A 315 SER cc_start: 0.8781 (m) cc_final: 0.8495 (p) REVERT: A 343 LYS cc_start: 0.9062 (tttp) cc_final: 0.8748 (tptp) REVERT: A 943 MET cc_start: 0.8467 (tmm) cc_final: 0.8171 (tmm) REVERT: B 138 MET cc_start: 0.8198 (mmm) cc_final: 0.7799 (mmm) REVERT: B 315 SER cc_start: 0.8784 (m) cc_final: 0.8494 (p) REVERT: B 343 LYS cc_start: 0.9063 (tttp) cc_final: 0.8749 (tptp) REVERT: B 943 MET cc_start: 0.8466 (tmm) cc_final: 0.8171 (tmm) outliers start: 12 outliers final: 6 residues processed: 142 average time/residue: 0.2365 time to fit residues: 52.9600 Evaluate side-chains 116 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 700 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.0170 chunk 127 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15176 Z= 0.181 Angle : 0.589 9.777 20584 Z= 0.290 Chirality : 0.045 0.588 2420 Planarity : 0.004 0.049 2540 Dihedral : 5.775 48.038 2346 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.98 % Favored : 90.69 % Rotamer: Outliers : 1.78 % Allowed : 13.74 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1848 helix: -0.51 (0.17), residues: 922 sheet: -0.73 (0.37), residues: 168 loop : -2.73 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 515 HIS 0.012 0.001 HIS B 995 PHE 0.010 0.001 PHE B 555 TYR 0.011 0.001 TYR A 243 ARG 0.003 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8152 (mmm) cc_final: 0.7898 (mmm) REVERT: A 325 MET cc_start: 0.8576 (mmm) cc_final: 0.8189 (mmm) REVERT: A 343 LYS cc_start: 0.9052 (tttp) cc_final: 0.8733 (tptp) REVERT: A 348 MET cc_start: 0.8590 (mmt) cc_final: 0.8250 (ptt) REVERT: A 672 GLU cc_start: 0.8446 (tt0) cc_final: 0.8110 (tm-30) REVERT: A 943 MET cc_start: 0.8503 (tmm) cc_final: 0.8169 (tmm) REVERT: B 138 MET cc_start: 0.8146 (mmm) cc_final: 0.7894 (mmm) REVERT: B 325 MET cc_start: 0.8576 (mmm) cc_final: 0.8190 (mmm) REVERT: B 343 LYS cc_start: 0.9052 (tttp) cc_final: 0.8733 (tptp) REVERT: B 348 MET cc_start: 0.8591 (mmt) cc_final: 0.8253 (ptt) REVERT: B 672 GLU cc_start: 0.8450 (tt0) cc_final: 0.8112 (tm-30) REVERT: B 943 MET cc_start: 0.8500 (tmm) cc_final: 0.8168 (tmm) outliers start: 28 outliers final: 16 residues processed: 142 average time/residue: 0.2293 time to fit residues: 51.7304 Evaluate side-chains 124 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 700 HIS Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.0030 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 0.0060 chunk 74 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 overall best weight: 0.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15176 Z= 0.124 Angle : 0.556 10.505 20584 Z= 0.271 Chirality : 0.043 0.551 2420 Planarity : 0.003 0.047 2540 Dihedral : 5.318 46.256 2346 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.23 % Favored : 91.45 % Rotamer: Outliers : 0.89 % Allowed : 15.39 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1848 helix: 0.04 (0.17), residues: 940 sheet: -0.51 (0.38), residues: 166 loop : -2.59 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 515 HIS 0.007 0.000 HIS B 995 PHE 0.010 0.001 PHE B 555 TYR 0.009 0.001 TYR B 663 ARG 0.003 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8595 (mmm) cc_final: 0.8149 (mmm) REVERT: A 343 LYS cc_start: 0.9051 (tttp) cc_final: 0.8681 (tptp) REVERT: A 348 MET cc_start: 0.8564 (mmt) cc_final: 0.8215 (ptt) REVERT: A 644 MET cc_start: 0.8964 (mtp) cc_final: 0.8759 (mtp) REVERT: A 672 GLU cc_start: 0.8406 (tt0) cc_final: 0.8118 (tm-30) REVERT: A 943 MET cc_start: 0.8529 (tmm) cc_final: 0.8145 (tmm) REVERT: A 1031 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6638 (ptm160) REVERT: B 325 MET cc_start: 0.8595 (mmm) cc_final: 0.8146 (mmm) REVERT: B 343 LYS cc_start: 0.9051 (tttp) cc_final: 0.8680 (tptp) REVERT: B 348 MET cc_start: 0.8569 (mmt) cc_final: 0.8214 (ptt) REVERT: B 644 MET cc_start: 0.8964 (mtp) cc_final: 0.8762 (mtp) REVERT: B 672 GLU cc_start: 0.8407 (tt0) cc_final: 0.8116 (tm-30) REVERT: B 943 MET cc_start: 0.8529 (tmm) cc_final: 0.8144 (tmm) REVERT: B 1031 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6639 (ptm160) outliers start: 14 outliers final: 10 residues processed: 150 average time/residue: 0.2424 time to fit residues: 55.9666 Evaluate side-chains 122 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 149 optimal weight: 0.0570 chunk 83 optimal weight: 0.0870 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15176 Z= 0.139 Angle : 0.549 9.905 20584 Z= 0.267 Chirality : 0.043 0.552 2420 Planarity : 0.003 0.044 2540 Dihedral : 4.748 41.211 2342 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.77 % Favored : 90.91 % Rotamer: Outliers : 1.78 % Allowed : 15.52 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1848 helix: 0.60 (0.18), residues: 940 sheet: -0.63 (0.37), residues: 172 loop : -2.44 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 515 HIS 0.005 0.001 HIS B 995 PHE 0.008 0.001 PHE B 555 TYR 0.010 0.001 TYR A 243 ARG 0.002 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9025 (tttp) cc_final: 0.8724 (tptp) REVERT: A 348 MET cc_start: 0.8574 (mmt) cc_final: 0.8255 (ptt) REVERT: A 536 SER cc_start: 0.9083 (m) cc_final: 0.8866 (t) REVERT: A 672 GLU cc_start: 0.8416 (tt0) cc_final: 0.8142 (tm-30) REVERT: A 943 MET cc_start: 0.8485 (tmm) cc_final: 0.8095 (tmm) REVERT: B 343 LYS cc_start: 0.9024 (tttp) cc_final: 0.8723 (tptp) REVERT: B 348 MET cc_start: 0.8575 (mmt) cc_final: 0.8257 (ptt) REVERT: B 536 SER cc_start: 0.9082 (m) cc_final: 0.8864 (t) REVERT: B 672 GLU cc_start: 0.8416 (tt0) cc_final: 0.8142 (tm-30) REVERT: B 943 MET cc_start: 0.8487 (tmm) cc_final: 0.8096 (tmm) outliers start: 28 outliers final: 12 residues processed: 140 average time/residue: 0.2212 time to fit residues: 48.2611 Evaluate side-chains 126 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15176 Z= 0.257 Angle : 0.607 10.697 20584 Z= 0.299 Chirality : 0.046 0.559 2420 Planarity : 0.004 0.043 2540 Dihedral : 4.876 40.984 2342 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.74 % Favored : 89.83 % Rotamer: Outliers : 1.65 % Allowed : 16.16 % Favored : 82.19 % 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: -0.88 (0.20), residues: 1848 helix: 0.80 (0.18), residues: 950 sheet: -0.68 (0.37), residues: 172 loop : -2.51 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 515 HIS 0.003 0.001 HIS A 719 PHE 0.011 0.001 PHE B 227 TYR 0.013 0.001 TYR B 243 ARG 0.003 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8623 (mmm) cc_final: 0.8313 (mmm) REVERT: A 343 LYS cc_start: 0.9075 (tttp) cc_final: 0.8680 (tptp) REVERT: A 348 MET cc_start: 0.8641 (mmt) cc_final: 0.8277 (ptt) REVERT: A 597 MET cc_start: 0.9107 (tpp) cc_final: 0.8880 (tpp) REVERT: A 672 GLU cc_start: 0.8452 (tt0) cc_final: 0.8163 (tm-30) REVERT: A 943 MET cc_start: 0.8506 (tmm) cc_final: 0.8115 (tmm) REVERT: B 325 MET cc_start: 0.8625 (mmm) cc_final: 0.8314 (mmm) REVERT: B 343 LYS cc_start: 0.9073 (tttp) cc_final: 0.8678 (tptp) REVERT: B 348 MET cc_start: 0.8644 (mmt) cc_final: 0.8279 (ptt) REVERT: B 597 MET cc_start: 0.9110 (tpp) cc_final: 0.8883 (tpp) REVERT: B 672 GLU cc_start: 0.8450 (tt0) cc_final: 0.8161 (tm-30) REVERT: B 943 MET cc_start: 0.8507 (tmm) cc_final: 0.8115 (tmm) outliers start: 26 outliers final: 18 residues processed: 134 average time/residue: 0.2280 time to fit residues: 49.5930 Evaluate side-chains 120 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15176 Z= 0.151 Angle : 0.562 9.846 20584 Z= 0.275 Chirality : 0.044 0.535 2420 Planarity : 0.003 0.044 2540 Dihedral : 4.766 41.911 2342 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.33 % Favored : 91.23 % Rotamer: Outliers : 0.76 % Allowed : 16.79 % Favored : 82.44 % 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: -0.70 (0.20), residues: 1848 helix: 0.95 (0.18), residues: 950 sheet: -0.59 (0.38), residues: 172 loop : -2.44 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 515 HIS 0.003 0.001 HIS A 995 PHE 0.008 0.001 PHE A 555 TYR 0.010 0.001 TYR A 243 ARG 0.002 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9092 (tttp) cc_final: 0.8692 (tptp) REVERT: A 348 MET cc_start: 0.8615 (mmt) cc_final: 0.8265 (ptt) REVERT: A 597 MET cc_start: 0.9041 (tpp) cc_final: 0.8812 (tpp) REVERT: A 672 GLU cc_start: 0.8389 (tt0) cc_final: 0.8123 (tm-30) REVERT: A 943 MET cc_start: 0.8534 (tmm) cc_final: 0.8140 (tmm) REVERT: B 343 LYS cc_start: 0.9090 (tttp) cc_final: 0.8691 (tptp) REVERT: B 348 MET cc_start: 0.8619 (mmt) cc_final: 0.8264 (ptt) REVERT: B 597 MET cc_start: 0.9042 (tpp) cc_final: 0.8815 (tpp) REVERT: B 672 GLU cc_start: 0.8391 (tt0) cc_final: 0.8124 (tm-30) REVERT: B 943 MET cc_start: 0.8541 (tmm) cc_final: 0.8145 (tmm) outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.2152 time to fit residues: 43.0049 Evaluate side-chains 120 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15176 Z= 0.193 Angle : 0.584 9.709 20584 Z= 0.283 Chirality : 0.044 0.537 2420 Planarity : 0.003 0.043 2540 Dihedral : 4.733 41.331 2342 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.74 % Favored : 89.83 % Rotamer: Outliers : 1.53 % Allowed : 16.54 % Favored : 81.93 % 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: -0.58 (0.20), residues: 1848 helix: 1.08 (0.18), residues: 954 sheet: -0.56 (0.38), residues: 172 loop : -2.43 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 515 HIS 0.003 0.001 HIS A 995 PHE 0.008 0.001 PHE A 227 TYR 0.010 0.001 TYR A 243 ARG 0.002 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9102 (tttp) cc_final: 0.8730 (tptp) REVERT: A 348 MET cc_start: 0.8586 (mmt) cc_final: 0.8210 (ptt) REVERT: A 672 GLU cc_start: 0.8418 (tt0) cc_final: 0.8150 (tm-30) REVERT: A 943 MET cc_start: 0.8539 (tmm) cc_final: 0.8146 (tmm) REVERT: B 343 LYS cc_start: 0.9102 (tttp) cc_final: 0.8731 (tptp) REVERT: B 348 MET cc_start: 0.8586 (mmt) cc_final: 0.8212 (ptt) REVERT: B 672 GLU cc_start: 0.8417 (tt0) cc_final: 0.8149 (tm-30) REVERT: B 943 MET cc_start: 0.8547 (tmm) cc_final: 0.8152 (tmm) outliers start: 24 outliers final: 16 residues processed: 130 average time/residue: 0.2169 time to fit residues: 45.4850 Evaluate side-chains 126 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15176 Z= 0.163 Angle : 0.580 10.029 20584 Z= 0.279 Chirality : 0.044 0.529 2420 Planarity : 0.003 0.043 2540 Dihedral : 4.707 41.750 2342 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.66 % Favored : 90.91 % Rotamer: Outliers : 0.89 % Allowed : 16.79 % Favored : 82.32 % 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: -0.49 (0.20), residues: 1848 helix: 1.14 (0.18), residues: 954 sheet: -0.50 (0.38), residues: 172 loop : -2.38 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 515 HIS 0.003 0.001 HIS A 995 PHE 0.008 0.001 PHE A 227 TYR 0.009 0.001 TYR A 243 ARG 0.002 0.000 ARG A 622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.9115 (tttp) cc_final: 0.8738 (tptp) REVERT: A 672 GLU cc_start: 0.8361 (tt0) cc_final: 0.8105 (tm-30) REVERT: A 943 MET cc_start: 0.8548 (tmm) cc_final: 0.8139 (tmm) REVERT: B 343 LYS cc_start: 0.9115 (tttp) cc_final: 0.8739 (tptp) REVERT: B 672 GLU cc_start: 0.8361 (tt0) cc_final: 0.8106 (tm-30) REVERT: B 943 MET cc_start: 0.8555 (tmm) cc_final: 0.8143 (tmm) outliers start: 14 outliers final: 14 residues processed: 124 average time/residue: 0.2138 time to fit residues: 43.2866 Evaluate side-chains 126 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.068963 restraints weight = 31703.634| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.23 r_work: 0.2776 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15176 Z= 0.177 Angle : 0.579 9.884 20584 Z= 0.281 Chirality : 0.044 0.528 2420 Planarity : 0.003 0.042 2540 Dihedral : 4.679 41.481 2342 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.58 % Favored : 89.99 % Rotamer: Outliers : 1.02 % Allowed : 16.92 % Favored : 82.06 % 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: -0.39 (0.20), residues: 1848 helix: 1.25 (0.18), residues: 954 sheet: -0.47 (0.38), residues: 172 loop : -2.38 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 515 HIS 0.003 0.001 HIS A 995 PHE 0.008 0.001 PHE A 227 TYR 0.009 0.001 TYR A 243 ARG 0.002 0.000 ARG A 622 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.65 seconds wall clock time: 49 minutes 46.09 seconds (2986.09 seconds total)