Starting phenix.real_space_refine on Wed Mar 20 16:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz9_24755/03_2024/7rz9_24755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz9_24755/03_2024/7rz9_24755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz9_24755/03_2024/7rz9_24755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz9_24755/03_2024/7rz9_24755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz9_24755/03_2024/7rz9_24755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz9_24755/03_2024/7rz9_24755.pdb" } resolution = 4.15 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 17952 2.51 5 N 4628 2.21 5 O 5210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1089": "NH1" <-> "NH2" Residue "A ARG 1111": "NH1" <-> "NH2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1089": "NH1" <-> "NH2" Residue "C ARG 1111": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27934 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7713 Classifications: {'peptide': 981} Link IDs: {'PCIS': 4, 'PTRANS': 24, 'TRANS': 952} Chain breaks: 3 Chain: "B" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6254 Classifications: {'peptide': 794} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 770} Chain breaks: 1 Chain: "C" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7713 Classifications: {'peptide': 981} Link IDs: {'PCIS': 4, 'PTRANS': 24, 'TRANS': 952} Chain breaks: 3 Chain: "D" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6254 Classifications: {'peptide': 794} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 770} Chain breaks: 1 Time building chain proxies: 15.33, per 1000 atoms: 0.55 Number of scatterers: 27934 At special positions: 0 Unit cell: (117.03, 166.83, 190.9, 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 144 16.00 O 5210 8.00 N 4628 7.00 C 17952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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 Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 5.2 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6524 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 38 sheets defined 47.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.705A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.662A pdb=" N THR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.540A pdb=" N LEU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.560A pdb=" N ALA A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.641A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.601A pdb=" N ASN A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.552A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 301 removed outlier: 3.709A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.944A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.888A pdb=" N LEU A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.707A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.937A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 4.093A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 627 removed outlier: 3.684A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.570A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.953A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 removed outlier: 3.645A pdb=" N MET A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.526A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.889A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.642A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.520A pdb=" N GLY A 779 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 780 " --> pdb=" O ASP A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 780' Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.995A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1029 removed outlier: 3.719A pdb=" N THR A1024 " --> pdb=" O LEU A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1117 removed outlier: 3.823A pdb=" N ALA A1117 " --> pdb=" O PHE A1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1113 through 1117' Processing helix chain 'A' and resid 1118 through 1147 removed outlier: 4.140A pdb=" N GLY A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1194 removed outlier: 4.079A pdb=" N VAL A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A1173 " --> pdb=" O PHE A1169 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A1186 " --> pdb=" O MET A1182 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A1187 " --> pdb=" O MET A1183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A1190 " --> pdb=" O GLN A1186 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A1193 " --> pdb=" O GLN A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1233 removed outlier: 3.731A pdb=" N PHE A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A1225 " --> pdb=" O MET A1221 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A1230 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.720A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 removed outlier: 3.524A pdb=" N GLY B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.868A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.912A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.777A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 3.786A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.674A pdb=" N ASN B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.408A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.628A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.604A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.759A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.652A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.748A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.649A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.697A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.502A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.619A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.799A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.694A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 674 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.783A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 removed outlier: 3.946A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 754 removed outlier: 3.719A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.692A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 781 Processing helix chain 'B' and resid 792 through 820 removed outlier: 4.039A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.704A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.660A pdb=" N THR C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.540A pdb=" N LEU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.560A pdb=" N ALA C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.640A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.601A pdb=" N ASN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.552A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 301 removed outlier: 3.710A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 335 removed outlier: 3.945A pdb=" N VAL C 327 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.887A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.706A pdb=" N HIS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.936A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 4.093A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 627 removed outlier: 3.684A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 636 through 641 removed outlier: 3.570A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.953A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 676 removed outlier: 3.645A pdb=" N MET C 674 " --> pdb=" O MET C 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 removed outlier: 3.526A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 694 " --> pdb=" O VAL C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.889A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.642A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 780 removed outlier: 3.520A pdb=" N GLY C 779 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 780 " --> pdb=" O ASP C 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 776 through 780' Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.994A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1029 removed outlier: 3.719A pdb=" N THR C1024 " --> pdb=" O LEU C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1117 removed outlier: 3.823A pdb=" N ALA C1117 " --> pdb=" O PHE C1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1113 through 1117' Processing helix chain 'C' and resid 1118 through 1147 removed outlier: 4.140A pdb=" N GLY C1123 " --> pdb=" O ALA C1119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C1124 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1194 removed outlier: 4.079A pdb=" N VAL C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C1173 " --> pdb=" O PHE C1169 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1179 " --> pdb=" O LEU C1175 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C1184 " --> pdb=" O ALA C1180 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C1186 " --> pdb=" O MET C1182 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C1187 " --> pdb=" O MET C1183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C1190 " --> pdb=" O GLN C1186 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C1193 " --> pdb=" O GLN C1189 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1233 removed outlier: 3.732A pdb=" N PHE C1217 " --> pdb=" O ALA C1213 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C1225 " --> pdb=" O MET C1221 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C1226 " --> pdb=" O ALA C1222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C1228 " --> pdb=" O SER C1224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C1230 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C1231 " --> pdb=" O THR C1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.720A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 67 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.868A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.913A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 157 removed outlier: 3.777A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 187 removed outlier: 3.786A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.673A pdb=" N ASN D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 removed outlier: 4.409A pdb=" N PHE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.628A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 260 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.604A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.758A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.651A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.749A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.648A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.697A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.501A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.619A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.799A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.693A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 674 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.783A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 712 removed outlier: 3.947A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 754 removed outlier: 3.718A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.693A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 781 Processing helix chain 'D' and resid 792 through 820 removed outlier: 4.041A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE D 812 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.691A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.691A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 164 removed outlier: 8.657A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 363 removed outlier: 3.871A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.918A pdb=" N LYS A 441 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 498 removed outlier: 7.207A pdb=" N SER A 492 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR A 736 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 734 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.063A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1036 through 1039 removed outlier: 3.660A pdb=" N HIS A1092 " --> pdb=" O CYS A1099 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A1099 " --> pdb=" O HIS A1092 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 47 removed outlier: 10.646A pdb=" N ALA B 72 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN B 13 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 164 removed outlier: 7.073A pdb=" N PHE B 133 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 338 through 339 removed outlier: 4.150A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.178A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'B' and resid 451 through 454 removed outlier: 3.712A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 454 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE B 459 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.110A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.456A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.691A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.691A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 159 through 164 removed outlier: 8.658A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC6, first strand: chain 'C' and resid 358 through 363 removed outlier: 3.870A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.918A pdb=" N LYS C 441 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC9, first strand: chain 'C' and resid 489 through 498 removed outlier: 7.208A pdb=" N SER C 492 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR C 736 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE C 734 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.063A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1036 through 1039 removed outlier: 3.661A pdb=" N HIS C1092 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS C1099 " --> pdb=" O HIS C1092 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 42 through 47 removed outlier: 10.647A pdb=" N ALA D 72 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN D 13 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE D 74 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.073A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 338 through 339 removed outlier: 4.150A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.178A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD8, first strand: chain 'D' and resid 451 through 454 removed outlier: 3.712A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 454 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 459 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE1, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.109A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.456A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3381 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: 9.48 Time building geometry restraints manager: 11.22 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: 8806 1.34 - 1.46: 6824 1.46 - 1.58: 12678 1.58 - 1.70: 0 1.70 - 1.82: 230 Bond restraints: 28538 Sorted by residual: bond pdb=" N SER B 388 " pdb=" CA SER B 388 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.17e-02 7.31e+03 6.68e+00 bond pdb=" N SER D 388 " pdb=" CA SER D 388 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.17e-02 7.31e+03 6.61e+00 bond pdb=" CB PRO D 520 " pdb=" CG PRO D 520 " ideal model delta sigma weight residual 1.492 1.378 0.114 5.00e-02 4.00e+02 5.22e+00 bond pdb=" CB PRO B 520 " pdb=" CG PRO B 520 " ideal model delta sigma weight residual 1.492 1.378 0.114 5.00e-02 4.00e+02 5.16e+00 bond pdb=" N SER C1154 " pdb=" CA SER C1154 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.04e+00 ... (remaining 28533 not shown) Histogram of bond angle deviations from ideal: 97.53 - 104.96: 375 104.96 - 112.40: 14363 112.40 - 119.83: 10004 119.83 - 127.26: 13564 127.26 - 134.70: 276 Bond angle restraints: 38582 Sorted by residual: angle pdb=" N GLY B 417 " pdb=" CA GLY B 417 " pdb=" C GLY B 417 " ideal model delta sigma weight residual 111.67 117.13 -5.46 9.20e-01 1.18e+00 3.52e+01 angle pdb=" N GLY D 417 " pdb=" CA GLY D 417 " pdb=" C GLY D 417 " ideal model delta sigma weight residual 111.67 117.09 -5.42 9.20e-01 1.18e+00 3.48e+01 angle pdb=" C THR B 387 " pdb=" N SER B 388 " pdb=" CA SER B 388 " ideal model delta sigma weight residual 121.19 130.06 -8.87 1.59e+00 3.96e-01 3.12e+01 angle pdb=" C THR D 387 " pdb=" N SER D 388 " pdb=" CA SER D 388 " ideal model delta sigma weight residual 121.19 130.06 -8.87 1.59e+00 3.96e-01 3.11e+01 angle pdb=" CA PRO D 679 " pdb=" C PRO D 679 " pdb=" O PRO D 679 " ideal model delta sigma weight residual 122.15 114.96 7.19 1.32e+00 5.74e-01 2.96e+01 ... (remaining 38577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 15850 14.82 - 29.64: 773 29.64 - 44.47: 235 44.47 - 59.29: 38 59.29 - 74.11: 14 Dihedral angle restraints: 16910 sinusoidal: 6696 harmonic: 10214 Sorted by residual: dihedral pdb=" CA GLU B 678 " pdb=" C GLU B 678 " pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta harmonic sigma weight residual 180.00 136.35 43.65 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" N PRO D 679 " pdb=" CA PRO D 679 " ideal model delta harmonic sigma weight residual 180.00 136.38 43.62 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta harmonic sigma weight residual -180.00 -142.24 -37.76 0 5.00e+00 4.00e-02 5.70e+01 ... (remaining 16907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3612 0.069 - 0.137: 624 0.137 - 0.206: 44 0.206 - 0.275: 8 0.275 - 0.344: 2 Chirality restraints: 4290 Sorted by residual: chirality pdb=" CB ILE C 304 " pdb=" CA ILE C 304 " pdb=" CG1 ILE C 304 " pdb=" CG2 ILE C 304 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE A 304 " pdb=" CA ILE A 304 " pdb=" CG1 ILE A 304 " pdb=" CG2 ILE A 304 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB VAL C 165 " pdb=" CA VAL C 165 " pdb=" CG1 VAL C 165 " pdb=" CG2 VAL C 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4287 not shown) Planarity restraints: 4866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.065 5.00e-02 4.00e+02 9.92e-02 1.57e+01 pdb=" N PRO D 99 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO B 99 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1195 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A1196 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A1196 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1196 " -0.034 5.00e-02 4.00e+02 ... (remaining 4863 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7553 2.79 - 3.32: 24674 3.32 - 3.85: 44667 3.85 - 4.37: 53086 4.37 - 4.90: 89382 Nonbonded interactions: 219362 Sorted by model distance: nonbonded pdb=" O MET D 33 " pdb=" OG SER D 37 " model vdw 2.264 2.440 nonbonded pdb=" O MET B 33 " pdb=" OG SER B 37 " model vdw 2.264 2.440 nonbonded pdb=" OG SER B 375 " pdb=" O ASP B 378 " model vdw 2.265 2.440 nonbonded pdb=" OG SER D 375 " pdb=" O ASP D 378 " model vdw 2.265 2.440 nonbonded pdb=" OE2 GLU C 25 " pdb=" OG1 THR C 281 " model vdw 2.308 2.440 ... (remaining 219357 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 'C' } ncs_group { reference = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.040 Extract box with map and model: 13.970 Check model and map are aligned: 0.600 Set scattering table: 0.210 Process input model: 72.970 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 28538 Z= 0.419 Angle : 0.978 12.546 38582 Z= 0.569 Chirality : 0.051 0.344 4290 Planarity : 0.007 0.099 4866 Dihedral : 10.412 74.110 10356 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.10), residues: 3526 helix: -4.17 (0.06), residues: 1656 sheet: -1.93 (0.26), residues: 396 loop : -2.69 (0.12), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C1032 HIS 0.009 0.003 HIS B 93 PHE 0.031 0.003 PHE A1091 TYR 0.016 0.002 TYR B 373 ARG 0.010 0.001 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 882 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.7442 (m-80) cc_final: 0.7008 (m-80) REVERT: A 138 ASP cc_start: 0.8432 (t70) cc_final: 0.7668 (t70) REVERT: A 140 ASP cc_start: 0.7655 (m-30) cc_final: 0.7449 (p0) REVERT: A 172 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7610 (pttt) REVERT: A 186 LEU cc_start: 0.8519 (mp) cc_final: 0.8191 (mt) REVERT: A 199 ASP cc_start: 0.8193 (m-30) cc_final: 0.7806 (t0) REVERT: A 262 TRP cc_start: 0.8966 (t-100) cc_final: 0.8571 (t-100) REVERT: A 346 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7828 (mtpt) REVERT: A 463 MET cc_start: 0.8141 (ttp) cc_final: 0.7838 (ttm) REVERT: A 493 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8636 (mmmm) REVERT: A 575 ASN cc_start: 0.8285 (m-40) cc_final: 0.7818 (t0) REVERT: A 591 ILE cc_start: 0.8799 (pt) cc_final: 0.8392 (pt) REVERT: A 638 ASP cc_start: 0.7853 (m-30) cc_final: 0.6433 (m-30) REVERT: A 1097 TYR cc_start: 0.7139 (m-10) cc_final: 0.6602 (m-80) REVERT: A 1151 LEU cc_start: 0.2678 (OUTLIER) cc_final: 0.2430 (tp) REVERT: A 1220 CYS cc_start: 0.8767 (m) cc_final: 0.8426 (m) REVERT: B 25 GLU cc_start: 0.8493 (mp0) cc_final: 0.7984 (mp0) REVERT: B 185 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7034 (tp30) REVERT: B 260 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7544 (mm-30) REVERT: B 449 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7791 (mttm) REVERT: B 519 ASP cc_start: 0.7859 (m-30) cc_final: 0.7554 (m-30) REVERT: B 528 CYS cc_start: 0.7924 (t) cc_final: 0.7700 (t) REVERT: B 533 TYR cc_start: 0.7971 (t80) cc_final: 0.7343 (t80) REVERT: B 587 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8058 (mm-40) REVERT: B 647 TYR cc_start: 0.8579 (p90) cc_final: 0.8179 (p90) REVERT: B 670 MET cc_start: 0.8021 (mtp) cc_final: 0.7818 (mtp) REVERT: B 686 THR cc_start: 0.8181 (m) cc_final: 0.7952 (p) REVERT: B 711 TYR cc_start: 0.7544 (t80) cc_final: 0.7132 (t80) REVERT: B 789 LEU cc_start: 0.8868 (tp) cc_final: 0.7871 (tp) REVERT: C 14 ILE cc_start: 0.8387 (pp) cc_final: 0.8103 (pt) REVERT: C 46 HIS cc_start: 0.7743 (t-90) cc_final: 0.7438 (t-90) REVERT: C 138 ASP cc_start: 0.8441 (t70) cc_final: 0.7739 (t70) REVERT: C 172 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7488 (pttt) REVERT: C 186 LEU cc_start: 0.8483 (mp) cc_final: 0.8164 (mt) REVERT: C 199 ASP cc_start: 0.8079 (m-30) cc_final: 0.7765 (t0) REVERT: C 262 TRP cc_start: 0.8919 (t-100) cc_final: 0.8552 (t-100) REVERT: C 278 ILE cc_start: 0.8738 (tt) cc_final: 0.8440 (pt) REVERT: C 299 LEU cc_start: 0.8131 (tp) cc_final: 0.7924 (tp) REVERT: C 363 LEU cc_start: 0.8426 (tp) cc_final: 0.8157 (tt) REVERT: C 425 CYS cc_start: 0.8898 (m) cc_final: 0.8357 (m) REVERT: C 476 ILE cc_start: 0.9021 (mt) cc_final: 0.8277 (mt) REVERT: C 537 SER cc_start: 0.8710 (m) cc_final: 0.8303 (t) REVERT: C 541 PHE cc_start: 0.8256 (t80) cc_final: 0.7962 (t80) REVERT: C 1093 THR cc_start: 0.8754 (t) cc_final: 0.8496 (m) REVERT: C 1097 TYR cc_start: 0.6821 (m-10) cc_final: 0.6382 (m-80) REVERT: C 1113 PHE cc_start: 0.6290 (t80) cc_final: 0.5855 (t80) REVERT: C 1134 LEU cc_start: 0.8624 (tp) cc_final: 0.8306 (tt) REVERT: C 1169 PHE cc_start: 0.6981 (m-10) cc_final: 0.6500 (m-80) REVERT: C 1182 MET cc_start: 0.8743 (mmm) cc_final: 0.8481 (tpt) REVERT: D 25 GLU cc_start: 0.8272 (mp0) cc_final: 0.7848 (mp0) REVERT: D 86 THR cc_start: 0.9194 (p) cc_final: 0.8934 (t) REVERT: D 168 ILE cc_start: 0.8706 (mm) cc_final: 0.8360 (mm) REVERT: D 300 ARG cc_start: 0.6162 (tpp-160) cc_final: 0.5868 (mmp-170) REVERT: D 380 MET cc_start: 0.7327 (ttt) cc_final: 0.6780 (ppp) REVERT: D 449 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7701 (mttm) REVERT: D 519 ASP cc_start: 0.8129 (m-30) cc_final: 0.7864 (m-30) REVERT: D 533 TYR cc_start: 0.7813 (t80) cc_final: 0.7499 (t80) REVERT: D 576 SER cc_start: 0.8388 (m) cc_final: 0.7926 (t) REVERT: D 580 SER cc_start: 0.9202 (m) cc_final: 0.8822 (p) REVERT: D 711 TYR cc_start: 0.7342 (t80) cc_final: 0.6887 (t80) REVERT: D 738 LYS cc_start: 0.7920 (tppp) cc_final: 0.7699 (tttp) outliers start: 8 outliers final: 2 residues processed: 890 average time/residue: 0.4053 time to fit residues: 561.7867 Evaluate side-chains 499 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 496 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 277 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A1037 GLN B 147 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 569 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN C1037 GLN D 54 ASN D 202 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28538 Z= 0.253 Angle : 0.593 6.356 38582 Z= 0.320 Chirality : 0.042 0.173 4290 Planarity : 0.005 0.074 4866 Dihedral : 5.345 44.183 3842 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.92 (0.12), residues: 3526 helix: -1.83 (0.10), residues: 1698 sheet: -1.63 (0.26), residues: 364 loop : -1.95 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 323 HIS 0.007 0.001 HIS D 93 PHE 0.022 0.002 PHE A1217 TYR 0.017 0.002 TYR C 373 ARG 0.007 0.000 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 649 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.8174 (pt) cc_final: 0.7694 (pt) REVERT: A 60 ASN cc_start: 0.8658 (m-40) cc_final: 0.8225 (t0) REVERT: A 71 TYR cc_start: 0.7377 (m-80) cc_final: 0.6985 (m-80) REVERT: A 78 ASP cc_start: 0.7397 (t70) cc_final: 0.6942 (t70) REVERT: A 140 ASP cc_start: 0.7461 (m-30) cc_final: 0.6809 (t70) REVERT: A 172 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7748 (pttt) REVERT: A 186 LEU cc_start: 0.8353 (mp) cc_final: 0.7903 (tp) REVERT: A 199 ASP cc_start: 0.8248 (m-30) cc_final: 0.7693 (t0) REVERT: A 262 TRP cc_start: 0.8785 (t-100) cc_final: 0.8447 (t-100) REVERT: A 346 LYS cc_start: 0.7865 (ptmt) cc_final: 0.7642 (mtpt) REVERT: A 363 LEU cc_start: 0.8477 (tp) cc_final: 0.8214 (tt) REVERT: A 425 CYS cc_start: 0.8715 (m) cc_final: 0.8362 (m) REVERT: A 476 ILE cc_start: 0.9098 (mt) cc_final: 0.8346 (mt) REVERT: A 670 MET cc_start: 0.8610 (ttm) cc_final: 0.8360 (ttm) REVERT: A 1016 ASN cc_start: 0.8198 (m-40) cc_final: 0.7985 (t0) REVERT: A 1097 TYR cc_start: 0.7174 (m-10) cc_final: 0.6770 (m-80) REVERT: A 1172 LEU cc_start: 0.7654 (mt) cc_final: 0.7266 (mt) REVERT: A 1206 TYR cc_start: 0.8300 (m-80) cc_final: 0.7942 (m-80) REVERT: A 1220 CYS cc_start: 0.8615 (m) cc_final: 0.8227 (m) REVERT: B 25 GLU cc_start: 0.8385 (mp0) cc_final: 0.7956 (mp0) REVERT: B 43 LEU cc_start: 0.7335 (mp) cc_final: 0.7134 (mp) REVERT: B 86 THR cc_start: 0.9151 (p) cc_final: 0.8904 (t) REVERT: B 185 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7299 (tp30) REVERT: B 260 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7571 (mm-30) REVERT: B 330 GLU cc_start: 0.7928 (tt0) cc_final: 0.7703 (tt0) REVERT: B 449 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7640 (mttm) REVERT: B 528 CYS cc_start: 0.7804 (t) cc_final: 0.7543 (t) REVERT: B 533 TYR cc_start: 0.7950 (t80) cc_final: 0.7710 (t80) REVERT: B 587 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8048 (mm110) REVERT: B 590 ASP cc_start: 0.6969 (p0) cc_final: 0.6586 (t0) REVERT: B 789 LEU cc_start: 0.8942 (tp) cc_final: 0.8245 (tp) REVERT: C 46 HIS cc_start: 0.7788 (t-90) cc_final: 0.7522 (t-90) REVERT: C 138 ASP cc_start: 0.8554 (t70) cc_final: 0.7966 (p0) REVERT: C 172 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7574 (pttt) REVERT: C 186 LEU cc_start: 0.8280 (mp) cc_final: 0.7847 (tp) REVERT: C 199 ASP cc_start: 0.8128 (m-30) cc_final: 0.7623 (t0) REVERT: C 346 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7745 (mttp) REVERT: C 363 LEU cc_start: 0.8501 (tp) cc_final: 0.8172 (tt) REVERT: C 425 CYS cc_start: 0.8684 (m) cc_final: 0.8435 (m) REVERT: C 476 ILE cc_start: 0.9124 (mt) cc_final: 0.8409 (mt) REVERT: C 541 PHE cc_start: 0.8445 (t80) cc_final: 0.8081 (t80) REVERT: C 587 GLN cc_start: 0.7729 (mm110) cc_final: 0.7104 (mp10) REVERT: C 638 ASP cc_start: 0.7786 (m-30) cc_final: 0.6482 (m-30) REVERT: C 1016 ASN cc_start: 0.7933 (m-40) cc_final: 0.7523 (t0) REVERT: C 1097 TYR cc_start: 0.6929 (m-10) cc_final: 0.6404 (m-80) REVERT: C 1113 PHE cc_start: 0.6402 (t80) cc_final: 0.5845 (t80) REVERT: C 1178 MET cc_start: 0.8568 (ttp) cc_final: 0.8288 (tmm) REVERT: C 1220 CYS cc_start: 0.8241 (m) cc_final: 0.7955 (m) REVERT: D 25 GLU cc_start: 0.8248 (mp0) cc_final: 0.7887 (mp0) REVERT: D 43 LEU cc_start: 0.7647 (mp) cc_final: 0.7447 (mp) REVERT: D 185 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7111 (tp30) REVERT: D 268 LYS cc_start: 0.8660 (mttt) cc_final: 0.8368 (mttm) REVERT: D 287 ASP cc_start: 0.8595 (m-30) cc_final: 0.8373 (m-30) REVERT: D 298 ASN cc_start: 0.8264 (m-40) cc_final: 0.7993 (m-40) REVERT: D 449 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7601 (mttm) REVERT: D 574 PHE cc_start: 0.7807 (t80) cc_final: 0.7580 (t80) REVERT: D 789 LEU cc_start: 0.8995 (tp) cc_final: 0.8684 (tp) outliers start: 1 outliers final: 0 residues processed: 650 average time/residue: 0.4014 time to fit residues: 416.8716 Evaluate side-chains 452 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 319 optimal weight: 0.0980 chunk 109 optimal weight: 0.8980 chunk 258 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 207 GLN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 ASN D 147 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28538 Z= 0.170 Angle : 0.507 6.176 38582 Z= 0.270 Chirality : 0.040 0.137 4290 Planarity : 0.004 0.064 4866 Dihedral : 4.752 40.894 3842 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.74 (0.13), residues: 3526 helix: -0.51 (0.12), residues: 1706 sheet: -1.59 (0.25), residues: 402 loop : -1.69 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 323 HIS 0.005 0.001 HIS C1092 PHE 0.023 0.001 PHE A 101 TYR 0.014 0.001 TYR A 373 ARG 0.008 0.000 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 3.131 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: A 60 ASN cc_start: 0.8510 (m-40) cc_final: 0.8265 (t0) REVERT: A 71 TYR cc_start: 0.7232 (m-80) cc_final: 0.7003 (m-80) REVERT: A 78 ASP cc_start: 0.7293 (t70) cc_final: 0.6717 (t70) REVERT: A 140 ASP cc_start: 0.7375 (m-30) cc_final: 0.6753 (t70) REVERT: A 172 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7609 (ptmt) REVERT: A 186 LEU cc_start: 0.8296 (mp) cc_final: 0.7851 (tp) REVERT: A 199 ASP cc_start: 0.8122 (m-30) cc_final: 0.7620 (t0) REVERT: A 325 GLN cc_start: 0.5921 (tt0) cc_final: 0.5173 (tt0) REVERT: A 361 MET cc_start: 0.7674 (mmm) cc_final: 0.7400 (mmm) REVERT: A 362 GLU cc_start: 0.8313 (tt0) cc_final: 0.8098 (tt0) REVERT: A 425 CYS cc_start: 0.8612 (m) cc_final: 0.8393 (m) REVERT: A 476 ILE cc_start: 0.9100 (mt) cc_final: 0.8349 (mt) REVERT: A 503 MET cc_start: 0.8373 (ttm) cc_final: 0.7971 (ttp) REVERT: A 1016 ASN cc_start: 0.8214 (m-40) cc_final: 0.7843 (t0) REVERT: A 1097 TYR cc_start: 0.7191 (m-10) cc_final: 0.6548 (m-80) REVERT: A 1113 PHE cc_start: 0.6698 (t80) cc_final: 0.5952 (t80) REVERT: A 1206 TYR cc_start: 0.8320 (m-80) cc_final: 0.7912 (m-80) REVERT: A 1220 CYS cc_start: 0.8510 (m) cc_final: 0.8188 (m) REVERT: B 25 GLU cc_start: 0.8439 (mp0) cc_final: 0.7946 (mp0) REVERT: B 86 THR cc_start: 0.9145 (p) cc_final: 0.8898 (t) REVERT: B 185 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7193 (tp30) REVERT: B 260 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7553 (mm-30) REVERT: B 287 ASP cc_start: 0.8690 (m-30) cc_final: 0.8413 (m-30) REVERT: B 334 LYS cc_start: 0.7487 (mptt) cc_final: 0.7237 (mmtp) REVERT: B 449 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7565 (mttm) REVERT: B 528 CYS cc_start: 0.7715 (t) cc_final: 0.7459 (t) REVERT: B 587 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7705 (mp10) REVERT: B 789 LEU cc_start: 0.8999 (tp) cc_final: 0.8189 (tp) REVERT: C 46 HIS cc_start: 0.7762 (t-90) cc_final: 0.7515 (t-90) REVERT: C 138 ASP cc_start: 0.8555 (t70) cc_final: 0.8002 (p0) REVERT: C 157 LYS cc_start: 0.8064 (tptt) cc_final: 0.7682 (tptm) REVERT: C 172 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7508 (ptmt) REVERT: C 186 LEU cc_start: 0.8285 (mp) cc_final: 0.7874 (tp) REVERT: C 199 ASP cc_start: 0.8012 (m-30) cc_final: 0.7563 (t0) REVERT: C 363 LEU cc_start: 0.8440 (tp) cc_final: 0.8200 (tt) REVERT: C 434 LYS cc_start: 0.8979 (mttm) cc_final: 0.8681 (mtpp) REVERT: C 476 ILE cc_start: 0.9103 (mt) cc_final: 0.8396 (mt) REVERT: C 541 PHE cc_start: 0.8469 (t80) cc_final: 0.8209 (t80) REVERT: C 1016 ASN cc_start: 0.7892 (m110) cc_final: 0.7571 (t0) REVERT: C 1097 TYR cc_start: 0.7044 (m-10) cc_final: 0.6431 (m-80) REVERT: C 1113 PHE cc_start: 0.6330 (t80) cc_final: 0.5806 (t80) REVERT: C 1220 CYS cc_start: 0.8112 (m) cc_final: 0.7903 (m) REVERT: D 25 GLU cc_start: 0.8246 (mp0) cc_final: 0.7914 (mp0) REVERT: D 168 ILE cc_start: 0.8375 (mm) cc_final: 0.8157 (mm) REVERT: D 287 ASP cc_start: 0.8657 (m-30) cc_final: 0.8321 (m-30) REVERT: D 298 ASN cc_start: 0.8167 (m-40) cc_final: 0.7918 (m-40) REVERT: D 405 TYR cc_start: 0.8264 (m-80) cc_final: 0.7551 (m-80) REVERT: D 449 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7469 (mttm) REVERT: D 481 ILE cc_start: 0.9368 (mt) cc_final: 0.8987 (pt) REVERT: D 574 PHE cc_start: 0.7811 (t80) cc_final: 0.7601 (t80) REVERT: D 628 ARG cc_start: 0.6659 (mtm110) cc_final: 0.5631 (ptp-170) REVERT: D 789 LEU cc_start: 0.8870 (tp) cc_final: 0.8606 (tp) outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.3668 time to fit residues: 337.3310 Evaluate side-chains 432 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 323 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 337 GLN B 435 HIS B 714 GLN C 355 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 337 GLN D 359 ASN D 435 HIS D 714 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 28538 Z= 0.505 Angle : 0.744 8.708 38582 Z= 0.391 Chirality : 0.049 0.330 4290 Planarity : 0.005 0.072 4866 Dihedral : 5.468 41.684 3842 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.03 % 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 (0.13), residues: 3526 helix: -0.29 (0.12), residues: 1678 sheet: -1.58 (0.25), residues: 402 loop : -1.64 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 323 HIS 0.011 0.002 HIS C 412 PHE 0.024 0.003 PHE C 495 TYR 0.028 0.002 TYR C 647 ARG 0.006 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8321 (mtmm) cc_final: 0.7688 (pttm) REVERT: A 186 LEU cc_start: 0.8449 (mp) cc_final: 0.7959 (tp) REVERT: A 262 TRP cc_start: 0.8833 (t-100) cc_final: 0.8519 (t-100) REVERT: A 265 LEU cc_start: 0.8150 (mt) cc_final: 0.7849 (mt) REVERT: A 346 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7527 (mttp) REVERT: A 425 CYS cc_start: 0.8655 (m) cc_final: 0.8414 (m) REVERT: A 476 ILE cc_start: 0.9270 (mt) cc_final: 0.8590 (mt) REVERT: A 1097 TYR cc_start: 0.7157 (m-10) cc_final: 0.6783 (m-80) REVERT: A 1113 PHE cc_start: 0.6811 (t80) cc_final: 0.6131 (t80) REVERT: A 1206 TYR cc_start: 0.8366 (m-80) cc_final: 0.8106 (m-80) REVERT: A 1217 PHE cc_start: 0.8302 (t80) cc_final: 0.7996 (t80) REVERT: A 1220 CYS cc_start: 0.8654 (m) cc_final: 0.8320 (m) REVERT: B 25 GLU cc_start: 0.8552 (mp0) cc_final: 0.7868 (mp0) REVERT: B 43 LEU cc_start: 0.7305 (mp) cc_final: 0.7024 (mp) REVERT: B 86 THR cc_start: 0.9105 (p) cc_final: 0.8851 (t) REVERT: B 287 ASP cc_start: 0.8838 (m-30) cc_final: 0.8455 (m-30) REVERT: B 533 TYR cc_start: 0.8222 (t80) cc_final: 0.7955 (t80) REVERT: B 587 GLN cc_start: 0.8686 (mm-40) cc_final: 0.7982 (mp10) REVERT: B 599 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7951 (mmt90) REVERT: B 789 LEU cc_start: 0.9077 (tp) cc_final: 0.8521 (tp) REVERT: C 46 HIS cc_start: 0.7841 (t-90) cc_final: 0.7495 (t-90) REVERT: C 60 ASN cc_start: 0.8891 (m-40) cc_final: 0.8446 (t0) REVERT: C 71 TYR cc_start: 0.7930 (m-10) cc_final: 0.7695 (m-10) REVERT: C 138 ASP cc_start: 0.8467 (t70) cc_final: 0.8149 (t0) REVERT: C 157 LYS cc_start: 0.8234 (tptt) cc_final: 0.7850 (tptm) REVERT: C 159 GLN cc_start: 0.7847 (mp-120) cc_final: 0.7647 (mp10) REVERT: C 172 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7747 (pttt) REVERT: C 186 LEU cc_start: 0.8270 (mp) cc_final: 0.8001 (tp) REVERT: C 262 TRP cc_start: 0.8806 (t-100) cc_final: 0.8541 (t-100) REVERT: C 434 LYS cc_start: 0.9065 (mttm) cc_final: 0.8707 (mtpp) REVERT: C 476 ILE cc_start: 0.9355 (mt) cc_final: 0.8742 (mt) REVERT: C 541 PHE cc_start: 0.8540 (t80) cc_final: 0.8309 (t80) REVERT: C 1016 ASN cc_start: 0.7899 (m110) cc_final: 0.7639 (t0) REVERT: C 1097 TYR cc_start: 0.7079 (m-10) cc_final: 0.6699 (m-80) REVERT: C 1113 PHE cc_start: 0.6571 (t80) cc_final: 0.6230 (t80) REVERT: C 1172 LEU cc_start: 0.8316 (mt) cc_final: 0.8099 (tp) REVERT: C 1220 CYS cc_start: 0.8271 (m) cc_final: 0.8040 (m) REVERT: D 25 GLU cc_start: 0.8442 (mp0) cc_final: 0.7986 (mp0) REVERT: D 43 LEU cc_start: 0.7234 (mp) cc_final: 0.6931 (mp) REVERT: D 159 GLN cc_start: 0.8412 (mp-120) cc_final: 0.8174 (mp10) REVERT: D 168 ILE cc_start: 0.8535 (mm) cc_final: 0.8294 (mm) REVERT: D 287 ASP cc_start: 0.8797 (m-30) cc_final: 0.8560 (m-30) REVERT: D 298 ASN cc_start: 0.8184 (m-40) cc_final: 0.7979 (t0) REVERT: D 422 GLU cc_start: 0.7250 (pm20) cc_final: 0.6888 (pm20) REVERT: D 629 MET cc_start: 0.7757 (mtm) cc_final: 0.6784 (ptp) REVERT: D 789 LEU cc_start: 0.9124 (tp) cc_final: 0.8756 (tp) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.3679 time to fit residues: 306.1034 Evaluate side-chains 403 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 435 HIS C 355 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 274 HIS D 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28538 Z= 0.173 Angle : 0.515 7.341 38582 Z= 0.271 Chirality : 0.041 0.211 4290 Planarity : 0.004 0.057 4866 Dihedral : 4.731 37.007 3842 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.91 (0.14), residues: 3526 helix: 0.50 (0.13), residues: 1678 sheet: -1.77 (0.24), residues: 432 loop : -1.49 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 323 HIS 0.008 0.001 HIS D 93 PHE 0.025 0.001 PHE C1217 TYR 0.016 0.001 TYR C 77 ARG 0.010 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7587 (pttt) REVERT: A 186 LEU cc_start: 0.8397 (mp) cc_final: 0.8005 (tp) REVERT: A 325 GLN cc_start: 0.6133 (tt0) cc_final: 0.5604 (tt0) REVERT: A 346 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7451 (mtpp) REVERT: A 476 ILE cc_start: 0.9086 (mt) cc_final: 0.8371 (mt) REVERT: A 670 MET cc_start: 0.8430 (ttm) cc_final: 0.8219 (mtm) REVERT: A 811 LEU cc_start: 0.8095 (tt) cc_final: 0.7716 (mt) REVERT: A 1097 TYR cc_start: 0.7181 (m-10) cc_final: 0.6540 (m-80) REVERT: A 1113 PHE cc_start: 0.6810 (t80) cc_final: 0.6048 (t80) REVERT: A 1206 TYR cc_start: 0.8407 (m-80) cc_final: 0.8051 (m-80) REVERT: A 1217 PHE cc_start: 0.8284 (t80) cc_final: 0.8024 (t80) REVERT: A 1220 CYS cc_start: 0.8559 (m) cc_final: 0.8197 (m) REVERT: B 25 GLU cc_start: 0.8438 (mp0) cc_final: 0.7810 (mp0) REVERT: B 43 LEU cc_start: 0.7126 (mp) cc_final: 0.6897 (mp) REVERT: B 86 THR cc_start: 0.9106 (p) cc_final: 0.8872 (t) REVERT: B 257 LYS cc_start: 0.7810 (mttt) cc_final: 0.7525 (mtmt) REVERT: B 260 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7656 (mm-30) REVERT: B 287 ASP cc_start: 0.8699 (m-30) cc_final: 0.8420 (m-30) REVERT: B 402 GLU cc_start: 0.8272 (tp30) cc_final: 0.7849 (tm-30) REVERT: B 450 TYR cc_start: 0.7948 (m-80) cc_final: 0.7744 (m-80) REVERT: B 599 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8166 (mmt90) REVERT: B 789 LEU cc_start: 0.8985 (tp) cc_final: 0.8375 (tp) REVERT: C 60 ASN cc_start: 0.8896 (m-40) cc_final: 0.8427 (t0) REVERT: C 138 ASP cc_start: 0.8413 (t70) cc_final: 0.7854 (p0) REVERT: C 157 LYS cc_start: 0.8164 (tptt) cc_final: 0.7753 (tptm) REVERT: C 172 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7546 (pttt) REVERT: C 186 LEU cc_start: 0.8305 (mp) cc_final: 0.7855 (tp) REVERT: C 363 LEU cc_start: 0.8519 (tp) cc_final: 0.8199 (tt) REVERT: C 434 LYS cc_start: 0.8920 (mttm) cc_final: 0.8642 (mtpp) REVERT: C 476 ILE cc_start: 0.9189 (mt) cc_final: 0.8547 (mt) REVERT: C 707 THR cc_start: 0.8845 (p) cc_final: 0.8632 (p) REVERT: C 1016 ASN cc_start: 0.7903 (m110) cc_final: 0.7648 (t0) REVERT: C 1097 TYR cc_start: 0.7132 (m-10) cc_final: 0.6527 (m-80) REVERT: C 1113 PHE cc_start: 0.6563 (t80) cc_final: 0.5839 (t80) REVERT: C 1126 TRP cc_start: 0.6973 (m100) cc_final: 0.5329 (t60) REVERT: C 1220 CYS cc_start: 0.8238 (m) cc_final: 0.7983 (m) REVERT: D 43 LEU cc_start: 0.7000 (mp) cc_final: 0.6762 (mp) REVERT: D 168 ILE cc_start: 0.8550 (mm) cc_final: 0.8295 (mm) REVERT: D 287 ASP cc_start: 0.8620 (m-30) cc_final: 0.8254 (m-30) REVERT: D 405 TYR cc_start: 0.8520 (m-80) cc_final: 0.8000 (m-80) REVERT: D 431 GLU cc_start: 0.7201 (tp30) cc_final: 0.6460 (tp30) REVERT: D 629 MET cc_start: 0.7739 (mtm) cc_final: 0.6762 (ptp) REVERT: D 789 LEU cc_start: 0.9038 (tp) cc_final: 0.8440 (tp) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.3760 time to fit residues: 326.6787 Evaluate side-chains 412 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS C 355 ASN C1016 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS D 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 28538 Z= 0.375 Angle : 0.640 8.013 38582 Z= 0.334 Chirality : 0.045 0.219 4290 Planarity : 0.004 0.062 4866 Dihedral : 5.002 35.979 3842 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.95 (0.14), residues: 3526 helix: 0.37 (0.13), residues: 1678 sheet: -1.57 (0.25), residues: 410 loop : -1.47 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 323 HIS 0.008 0.001 HIS A 412 PHE 0.020 0.002 PHE C 495 TYR 0.016 0.002 TYR A 77 ARG 0.009 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7511 (t70) cc_final: 0.7136 (t70) REVERT: A 140 ASP cc_start: 0.7520 (m-30) cc_final: 0.7131 (t70) REVERT: A 172 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7580 (pttm) REVERT: A 186 LEU cc_start: 0.8252 (mp) cc_final: 0.7803 (tp) REVERT: A 262 TRP cc_start: 0.8786 (t-100) cc_final: 0.8495 (t-100) REVERT: A 325 GLN cc_start: 0.6257 (tt0) cc_final: 0.5840 (tt0) REVERT: A 346 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7520 (mtpp) REVERT: A 414 MET cc_start: 0.3935 (ptp) cc_final: 0.3639 (ptp) REVERT: A 811 LEU cc_start: 0.8109 (tt) cc_final: 0.7801 (mt) REVERT: A 1097 TYR cc_start: 0.7152 (m-10) cc_final: 0.6596 (m-80) REVERT: A 1113 PHE cc_start: 0.6866 (t80) cc_final: 0.6024 (t80) REVERT: A 1206 TYR cc_start: 0.8491 (m-80) cc_final: 0.8184 (m-80) REVERT: A 1217 PHE cc_start: 0.8337 (t80) cc_final: 0.7998 (t80) REVERT: A 1220 CYS cc_start: 0.8608 (m) cc_final: 0.8287 (m) REVERT: B 25 GLU cc_start: 0.8553 (mp0) cc_final: 0.7891 (mp0) REVERT: B 93 HIS cc_start: 0.8144 (m170) cc_final: 0.7936 (m170) REVERT: B 287 ASP cc_start: 0.8732 (m-30) cc_final: 0.8508 (m-30) REVERT: B 298 ASN cc_start: 0.8027 (m-40) cc_final: 0.7818 (m-40) REVERT: B 314 ASP cc_start: 0.8026 (t0) cc_final: 0.7753 (p0) REVERT: B 450 TYR cc_start: 0.8094 (m-80) cc_final: 0.7828 (m-80) REVERT: B 789 LEU cc_start: 0.9021 (tp) cc_final: 0.8341 (tp) REVERT: C 60 ASN cc_start: 0.8890 (m-40) cc_final: 0.8563 (t0) REVERT: C 138 ASP cc_start: 0.8385 (t70) cc_final: 0.7793 (p0) REVERT: C 157 LYS cc_start: 0.8210 (tptt) cc_final: 0.7809 (tptm) REVERT: C 159 GLN cc_start: 0.7825 (mp-120) cc_final: 0.7398 (mp10) REVERT: C 172 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7562 (pttm) REVERT: C 186 LEU cc_start: 0.8264 (mp) cc_final: 0.7843 (tp) REVERT: C 262 TRP cc_start: 0.8739 (t-100) cc_final: 0.8476 (t-100) REVERT: C 363 LEU cc_start: 0.8521 (tp) cc_final: 0.8151 (tt) REVERT: C 541 PHE cc_start: 0.8355 (t80) cc_final: 0.8149 (t80) REVERT: C 1016 ASN cc_start: 0.8050 (m-40) cc_final: 0.7837 (t0) REVERT: C 1097 TYR cc_start: 0.7103 (m-10) cc_final: 0.6721 (m-80) REVERT: C 1113 PHE cc_start: 0.6699 (t80) cc_final: 0.6032 (t80) REVERT: C 1124 VAL cc_start: 0.7716 (t) cc_final: 0.7513 (p) REVERT: C 1172 LEU cc_start: 0.8326 (mt) cc_final: 0.8035 (mt) REVERT: C 1220 CYS cc_start: 0.8334 (m) cc_final: 0.8071 (m) REVERT: D 25 GLU cc_start: 0.8411 (mp0) cc_final: 0.8107 (mp0) REVERT: D 43 LEU cc_start: 0.6932 (mp) cc_final: 0.6707 (mp) REVERT: D 168 ILE cc_start: 0.8543 (mm) cc_final: 0.8275 (mm) REVERT: D 287 ASP cc_start: 0.8619 (m-30) cc_final: 0.8365 (m-30) REVERT: D 405 TYR cc_start: 0.8558 (m-80) cc_final: 0.8023 (m-80) REVERT: D 578 TRP cc_start: 0.8907 (t-100) cc_final: 0.8414 (t-100) REVERT: D 629 MET cc_start: 0.7750 (mtm) cc_final: 0.6845 (ptp) REVERT: D 789 LEU cc_start: 0.9053 (tp) cc_final: 0.8625 (tp) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3718 time to fit residues: 302.7585 Evaluate side-chains 400 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 435 HIS C 147 GLN C 355 ASN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 435 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28538 Z= 0.157 Angle : 0.511 6.931 38582 Z= 0.267 Chirality : 0.041 0.197 4290 Planarity : 0.004 0.054 4866 Dihedral : 4.546 32.313 3842 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 (0.14), residues: 3526 helix: 0.84 (0.13), residues: 1678 sheet: -1.85 (0.25), residues: 422 loop : -1.34 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 323 HIS 0.004 0.001 HIS B 93 PHE 0.030 0.001 PHE C1217 TYR 0.013 0.001 TYR C 77 ARG 0.004 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7427 (t70) cc_final: 0.7029 (t70) REVERT: A 140 ASP cc_start: 0.7455 (m-30) cc_final: 0.7246 (t70) REVERT: A 172 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7615 (pttt) REVERT: A 186 LEU cc_start: 0.8330 (mp) cc_final: 0.7893 (tp) REVERT: A 262 TRP cc_start: 0.8698 (t-100) cc_final: 0.8428 (t-100) REVERT: A 325 GLN cc_start: 0.6174 (tt0) cc_final: 0.5545 (tt0) REVERT: A 346 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7467 (mtpp) REVERT: A 355 ASN cc_start: 0.7127 (m-40) cc_final: 0.6417 (t0) REVERT: A 414 MET cc_start: 0.3902 (ptp) cc_final: 0.3621 (ptp) REVERT: A 503 MET cc_start: 0.7949 (ttp) cc_final: 0.7552 (ttp) REVERT: A 811 LEU cc_start: 0.8060 (tt) cc_final: 0.7749 (mt) REVERT: A 1097 TYR cc_start: 0.7144 (m-10) cc_final: 0.6611 (m-80) REVERT: A 1113 PHE cc_start: 0.6831 (t80) cc_final: 0.6180 (t80) REVERT: A 1206 TYR cc_start: 0.8513 (m-80) cc_final: 0.8140 (m-80) REVERT: A 1217 PHE cc_start: 0.8309 (t80) cc_final: 0.8018 (t80) REVERT: A 1220 CYS cc_start: 0.8552 (m) cc_final: 0.8219 (m) REVERT: B 43 LEU cc_start: 0.6881 (mp) cc_final: 0.6680 (mt) REVERT: B 93 HIS cc_start: 0.8112 (m170) cc_final: 0.7884 (m170) REVERT: B 189 GLU cc_start: 0.7499 (tp30) cc_final: 0.7122 (tp30) REVERT: B 287 ASP cc_start: 0.8692 (m-30) cc_final: 0.8458 (m-30) REVERT: B 298 ASN cc_start: 0.7936 (m-40) cc_final: 0.7731 (m-40) REVERT: B 314 ASP cc_start: 0.8031 (t0) cc_final: 0.7794 (p0) REVERT: B 402 GLU cc_start: 0.8258 (tp30) cc_final: 0.7860 (tm-30) REVERT: B 661 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7702 (ptp90) REVERT: B 789 LEU cc_start: 0.8931 (tp) cc_final: 0.8248 (tp) REVERT: C 60 ASN cc_start: 0.8859 (m-40) cc_final: 0.8580 (t0) REVERT: C 138 ASP cc_start: 0.8358 (t70) cc_final: 0.7835 (p0) REVERT: C 157 LYS cc_start: 0.8142 (tptt) cc_final: 0.7745 (tptm) REVERT: C 172 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7586 (pttt) REVERT: C 186 LEU cc_start: 0.8139 (mp) cc_final: 0.7710 (tp) REVERT: C 363 LEU cc_start: 0.8432 (tp) cc_final: 0.8176 (tt) REVERT: C 414 MET cc_start: 0.6602 (ttm) cc_final: 0.5785 (mpp) REVERT: C 707 THR cc_start: 0.8853 (p) cc_final: 0.8652 (p) REVERT: C 1097 TYR cc_start: 0.7075 (m-10) cc_final: 0.6525 (m-80) REVERT: C 1113 PHE cc_start: 0.6621 (t80) cc_final: 0.5783 (t80) REVERT: C 1126 TRP cc_start: 0.7090 (m100) cc_final: 0.5278 (t60) REVERT: C 1208 TRP cc_start: 0.8118 (p-90) cc_final: 0.7826 (p-90) REVERT: C 1217 PHE cc_start: 0.8267 (t80) cc_final: 0.7112 (t80) REVERT: C 1220 CYS cc_start: 0.8163 (m) cc_final: 0.7907 (m) REVERT: C 1221 MET cc_start: 0.7468 (mtt) cc_final: 0.7146 (mtt) REVERT: D 25 GLU cc_start: 0.8376 (mp0) cc_final: 0.7941 (pm20) REVERT: D 168 ILE cc_start: 0.8494 (mm) cc_final: 0.8239 (mm) REVERT: D 287 ASP cc_start: 0.8532 (m-30) cc_final: 0.8278 (m-30) REVERT: D 405 TYR cc_start: 0.8461 (m-80) cc_final: 0.7942 (m-80) REVERT: D 431 GLU cc_start: 0.7100 (tp30) cc_final: 0.6512 (tp30) REVERT: D 629 MET cc_start: 0.7716 (mtm) cc_final: 0.6686 (ptp) REVERT: D 789 LEU cc_start: 0.9019 (tp) cc_final: 0.8629 (tp) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.3661 time to fit residues: 306.4855 Evaluate side-chains 406 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.0270 chunk 136 optimal weight: 0.8980 chunk 203 optimal weight: 0.0570 chunk 102 optimal weight: 0.1980 chunk 67 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN C 355 ASN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 ASN D 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28538 Z= 0.136 Angle : 0.492 8.742 38582 Z= 0.256 Chirality : 0.040 0.187 4290 Planarity : 0.003 0.051 4866 Dihedral : 4.269 28.695 3842 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % 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: -0.35 (0.14), residues: 3526 helix: 1.05 (0.13), residues: 1688 sheet: -1.69 (0.24), residues: 426 loop : -1.29 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 323 HIS 0.002 0.001 HIS A 214 PHE 0.018 0.001 PHE B 74 TYR 0.013 0.001 TYR B 270 ARG 0.007 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7396 (t70) cc_final: 0.7066 (t70) REVERT: A 172 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7586 (pttt) REVERT: A 186 LEU cc_start: 0.8336 (mp) cc_final: 0.7933 (tp) REVERT: A 325 GLN cc_start: 0.6169 (tt0) cc_final: 0.5534 (tt0) REVERT: A 355 ASN cc_start: 0.7092 (m-40) cc_final: 0.6375 (t0) REVERT: A 361 MET cc_start: 0.7602 (mmm) cc_final: 0.7217 (mmm) REVERT: A 414 MET cc_start: 0.3754 (ptp) cc_final: 0.3548 (ptp) REVERT: A 425 CYS cc_start: 0.8625 (m) cc_final: 0.8345 (m) REVERT: A 476 ILE cc_start: 0.9212 (mt) cc_final: 0.8469 (mt) REVERT: A 503 MET cc_start: 0.7893 (ttp) cc_final: 0.7425 (ttp) REVERT: A 811 LEU cc_start: 0.8013 (tt) cc_final: 0.7738 (mt) REVERT: A 1097 TYR cc_start: 0.7117 (m-10) cc_final: 0.6577 (m-80) REVERT: A 1113 PHE cc_start: 0.6816 (t80) cc_final: 0.6126 (t80) REVERT: A 1206 TYR cc_start: 0.8510 (m-80) cc_final: 0.8097 (m-80) REVERT: A 1217 PHE cc_start: 0.8262 (t80) cc_final: 0.7945 (t80) REVERT: A 1220 CYS cc_start: 0.8374 (m) cc_final: 0.8084 (m) REVERT: B 25 GLU cc_start: 0.8386 (mp0) cc_final: 0.7846 (pm20) REVERT: B 287 ASP cc_start: 0.8698 (m-30) cc_final: 0.8483 (m-30) REVERT: B 298 ASN cc_start: 0.7903 (m-40) cc_final: 0.7675 (t0) REVERT: B 314 ASP cc_start: 0.8102 (t0) cc_final: 0.7847 (p0) REVERT: B 402 GLU cc_start: 0.8130 (tp30) cc_final: 0.7894 (tm-30) REVERT: B 661 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7698 (ptp90) REVERT: B 789 LEU cc_start: 0.8886 (tp) cc_final: 0.8214 (tp) REVERT: C 60 ASN cc_start: 0.8840 (m-40) cc_final: 0.8596 (t0) REVERT: C 138 ASP cc_start: 0.8350 (t70) cc_final: 0.7851 (p0) REVERT: C 157 LYS cc_start: 0.8093 (tptt) cc_final: 0.7718 (tptm) REVERT: C 172 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7563 (pttt) REVERT: C 186 LEU cc_start: 0.8288 (mp) cc_final: 0.7876 (tp) REVERT: C 363 LEU cc_start: 0.8414 (tp) cc_final: 0.8163 (tt) REVERT: C 410 LYS cc_start: 0.6046 (mmmt) cc_final: 0.5845 (mmmm) REVERT: C 425 CYS cc_start: 0.8547 (m) cc_final: 0.8298 (m) REVERT: C 1097 TYR cc_start: 0.7097 (m-10) cc_final: 0.6568 (m-80) REVERT: C 1113 PHE cc_start: 0.6596 (t80) cc_final: 0.5950 (t80) REVERT: C 1126 TRP cc_start: 0.6964 (m100) cc_final: 0.5266 (t60) REVERT: C 1217 PHE cc_start: 0.8234 (t80) cc_final: 0.7242 (t80) REVERT: D 25 GLU cc_start: 0.8351 (mp0) cc_final: 0.7857 (pm20) REVERT: D 168 ILE cc_start: 0.8490 (mm) cc_final: 0.8233 (mm) REVERT: D 287 ASP cc_start: 0.8652 (m-30) cc_final: 0.8211 (m-30) REVERT: D 405 TYR cc_start: 0.8636 (m-80) cc_final: 0.8142 (m-80) REVERT: D 518 LEU cc_start: 0.8821 (pp) cc_final: 0.8567 (pp) REVERT: D 629 MET cc_start: 0.7651 (mtm) cc_final: 0.6725 (ptp) REVERT: D 752 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8061 (ttmm) REVERT: D 789 LEU cc_start: 0.8991 (tp) cc_final: 0.8602 (tp) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.3666 time to fit residues: 315.3478 Evaluate side-chains 422 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 4.9990 chunk 326 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 249 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 287 optimal weight: 0.8980 chunk 300 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 714 GLN C 355 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28538 Z= 0.163 Angle : 0.505 8.392 38582 Z= 0.263 Chirality : 0.041 0.162 4290 Planarity : 0.004 0.083 4866 Dihedral : 4.269 27.908 3842 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3526 helix: 1.20 (0.13), residues: 1686 sheet: -1.65 (0.24), residues: 426 loop : -1.25 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 323 HIS 0.003 0.001 HIS B 93 PHE 0.047 0.001 PHE C1217 TYR 0.015 0.001 TYR A 700 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.7145 (m-80) cc_final: 0.6906 (m-80) REVERT: A 172 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7619 (pttt) REVERT: A 186 LEU cc_start: 0.8321 (mp) cc_final: 0.7946 (tp) REVERT: A 262 TRP cc_start: 0.8649 (t-100) cc_final: 0.8393 (t-100) REVERT: A 325 GLN cc_start: 0.6201 (tt0) cc_final: 0.5599 (tt0) REVERT: A 414 MET cc_start: 0.3751 (ptp) cc_final: 0.3543 (ptp) REVERT: A 425 CYS cc_start: 0.8566 (m) cc_final: 0.8282 (m) REVERT: A 476 ILE cc_start: 0.9096 (mt) cc_final: 0.8334 (mt) REVERT: A 811 LEU cc_start: 0.8027 (tt) cc_final: 0.7756 (mt) REVERT: A 1097 TYR cc_start: 0.7116 (m-10) cc_final: 0.6578 (m-80) REVERT: A 1113 PHE cc_start: 0.6729 (t80) cc_final: 0.6034 (t80) REVERT: A 1206 TYR cc_start: 0.8498 (m-80) cc_final: 0.8122 (m-80) REVERT: A 1217 PHE cc_start: 0.8277 (t80) cc_final: 0.7513 (t80) REVERT: A 1220 CYS cc_start: 0.8297 (m) cc_final: 0.7888 (m) REVERT: B 25 GLU cc_start: 0.8422 (mp0) cc_final: 0.7887 (pm20) REVERT: B 93 HIS cc_start: 0.8126 (m170) cc_final: 0.7907 (m170) REVERT: B 287 ASP cc_start: 0.8767 (m-30) cc_final: 0.8542 (m-30) REVERT: B 298 ASN cc_start: 0.7878 (m-40) cc_final: 0.7667 (t0) REVERT: B 314 ASP cc_start: 0.8123 (t0) cc_final: 0.7896 (p0) REVERT: B 518 LEU cc_start: 0.8742 (pp) cc_final: 0.8403 (pp) REVERT: B 587 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7991 (mm110) REVERT: B 661 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7709 (ptp90) REVERT: B 789 LEU cc_start: 0.8875 (tp) cc_final: 0.8217 (tp) REVERT: C 138 ASP cc_start: 0.8328 (t70) cc_final: 0.7866 (p0) REVERT: C 157 LYS cc_start: 0.8074 (tptt) cc_final: 0.7689 (tptm) REVERT: C 172 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7493 (pttm) REVERT: C 186 LEU cc_start: 0.8276 (mp) cc_final: 0.7889 (tp) REVERT: C 363 LEU cc_start: 0.8417 (tp) cc_final: 0.8123 (tt) REVERT: C 410 LYS cc_start: 0.6006 (mmmt) cc_final: 0.5797 (mmmm) REVERT: C 425 CYS cc_start: 0.8595 (m) cc_final: 0.8364 (m) REVERT: C 476 ILE cc_start: 0.9226 (mt) cc_final: 0.8511 (mt) REVERT: C 516 SER cc_start: 0.8985 (t) cc_final: 0.8559 (t) REVERT: C 519 ASP cc_start: 0.8561 (m-30) cc_final: 0.8315 (m-30) REVERT: C 542 LEU cc_start: 0.8430 (tp) cc_final: 0.8130 (tt) REVERT: C 1097 TYR cc_start: 0.7086 (m-10) cc_final: 0.6555 (m-80) REVERT: C 1113 PHE cc_start: 0.6581 (t80) cc_final: 0.5929 (t80) REVERT: C 1126 TRP cc_start: 0.7040 (m100) cc_final: 0.5269 (t60) REVERT: D 25 GLU cc_start: 0.8357 (mp0) cc_final: 0.7948 (pm20) REVERT: D 168 ILE cc_start: 0.8448 (mm) cc_final: 0.8156 (mm) REVERT: D 287 ASP cc_start: 0.8739 (m-30) cc_final: 0.8476 (m-30) REVERT: D 405 TYR cc_start: 0.8610 (m-80) cc_final: 0.8077 (m-80) REVERT: D 518 LEU cc_start: 0.8866 (pp) cc_final: 0.8587 (pp) REVERT: D 629 MET cc_start: 0.7660 (mtm) cc_final: 0.6662 (ptp) REVERT: D 789 LEU cc_start: 0.8952 (tp) cc_final: 0.8578 (tp) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.3724 time to fit residues: 311.9832 Evaluate side-chains 420 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 159 optimal weight: 0.0270 chunk 233 optimal weight: 1.9990 chunk 352 optimal weight: 0.9980 chunk 324 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 355 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 714 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN D 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28538 Z= 0.182 Angle : 0.512 8.332 38582 Z= 0.265 Chirality : 0.041 0.164 4290 Planarity : 0.004 0.079 4866 Dihedral : 4.279 27.627 3842 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % 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: -0.19 (0.14), residues: 3526 helix: 1.21 (0.13), residues: 1690 sheet: -1.60 (0.24), residues: 426 loop : -1.25 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 323 HIS 0.006 0.001 HIS B 93 PHE 0.032 0.001 PHE D 66 TYR 0.014 0.001 TYR B 77 ARG 0.004 0.000 ARG A 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7627 (pttt) REVERT: A 186 LEU cc_start: 0.8337 (mp) cc_final: 0.7713 (tt) REVERT: A 262 TRP cc_start: 0.8693 (t-100) cc_final: 0.8411 (t-100) REVERT: A 414 MET cc_start: 0.3755 (ptp) cc_final: 0.3526 (ptp) REVERT: A 425 CYS cc_start: 0.8564 (m) cc_final: 0.8291 (m) REVERT: A 476 ILE cc_start: 0.9123 (mt) cc_final: 0.8317 (mt) REVERT: A 541 PHE cc_start: 0.8408 (t80) cc_final: 0.8207 (t80) REVERT: A 811 LEU cc_start: 0.8034 (tt) cc_final: 0.7762 (mt) REVERT: A 1097 TYR cc_start: 0.7155 (m-10) cc_final: 0.6598 (m-80) REVERT: A 1113 PHE cc_start: 0.6731 (t80) cc_final: 0.5991 (t80) REVERT: A 1206 TYR cc_start: 0.8511 (m-80) cc_final: 0.8132 (m-80) REVERT: A 1217 PHE cc_start: 0.8272 (t80) cc_final: 0.7498 (t80) REVERT: A 1220 CYS cc_start: 0.8350 (m) cc_final: 0.8042 (m) REVERT: B 25 GLU cc_start: 0.8466 (mp0) cc_final: 0.7895 (pm20) REVERT: B 267 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6921 (tt0) REVERT: B 287 ASP cc_start: 0.8769 (m-30) cc_final: 0.8525 (m-30) REVERT: B 298 ASN cc_start: 0.7854 (m-40) cc_final: 0.7631 (t0) REVERT: B 314 ASP cc_start: 0.8146 (t0) cc_final: 0.7900 (p0) REVERT: B 330 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7874 (tt0) REVERT: B 587 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7698 (mp10) REVERT: B 661 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7742 (ptp90) REVERT: B 789 LEU cc_start: 0.8875 (tp) cc_final: 0.8172 (tp) REVERT: C 60 ASN cc_start: 0.8838 (m-40) cc_final: 0.8537 (t0) REVERT: C 138 ASP cc_start: 0.8375 (t70) cc_final: 0.7891 (p0) REVERT: C 157 LYS cc_start: 0.8048 (tptt) cc_final: 0.7684 (tptm) REVERT: C 172 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7584 (pttt) REVERT: C 186 LEU cc_start: 0.8326 (mp) cc_final: 0.7933 (tp) REVERT: C 262 TRP cc_start: 0.8658 (t-100) cc_final: 0.8405 (t-100) REVERT: C 363 LEU cc_start: 0.8393 (tp) cc_final: 0.8087 (tt) REVERT: C 414 MET cc_start: 0.6740 (ttm) cc_final: 0.5869 (mpp) REVERT: C 425 CYS cc_start: 0.8570 (m) cc_final: 0.8323 (m) REVERT: C 476 ILE cc_start: 0.9148 (mt) cc_final: 0.8408 (mt) REVERT: C 516 SER cc_start: 0.8921 (t) cc_final: 0.8463 (t) REVERT: C 519 ASP cc_start: 0.8554 (m-30) cc_final: 0.8299 (m-30) REVERT: C 542 LEU cc_start: 0.8395 (tp) cc_final: 0.8114 (tt) REVERT: C 1097 TYR cc_start: 0.7031 (m-10) cc_final: 0.6418 (m-80) REVERT: C 1113 PHE cc_start: 0.6745 (t80) cc_final: 0.6117 (t80) REVERT: C 1126 TRP cc_start: 0.7035 (m100) cc_final: 0.5269 (t60) REVERT: C 1217 PHE cc_start: 0.8188 (t80) cc_final: 0.7142 (t80) REVERT: D 25 GLU cc_start: 0.8350 (mp0) cc_final: 0.7905 (pm20) REVERT: D 168 ILE cc_start: 0.8429 (mm) cc_final: 0.8165 (mm) REVERT: D 287 ASP cc_start: 0.8696 (m-30) cc_final: 0.8344 (m-30) REVERT: D 405 TYR cc_start: 0.8566 (m-80) cc_final: 0.8156 (m-80) REVERT: D 518 LEU cc_start: 0.8883 (pp) cc_final: 0.8565 (pp) REVERT: D 629 MET cc_start: 0.7576 (mtm) cc_final: 0.6636 (ptp) REVERT: D 789 LEU cc_start: 0.8925 (tp) cc_final: 0.8553 (tp) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3529 time to fit residues: 291.9699 Evaluate side-chains 411 residues out of total 3022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 258 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 288 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 714 GLN C 355 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135850 restraints weight = 43452.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136288 restraints weight = 73639.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135429 restraints weight = 43021.656| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28538 Z= 0.161 Angle : 0.507 8.133 38582 Z= 0.263 Chirality : 0.041 0.185 4290 Planarity : 0.004 0.075 4866 Dihedral : 4.213 26.968 3842 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % 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: -0.12 (0.14), residues: 3526 helix: 1.27 (0.13), residues: 1690 sheet: -1.55 (0.24), residues: 424 loop : -1.24 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C1208 HIS 0.016 0.001 HIS B 93 PHE 0.046 0.001 PHE A1217 TYR 0.013 0.001 TYR A 77 ARG 0.006 0.000 ARG B 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6392.17 seconds wall clock time: 118 minutes 41.06 seconds (7121.06 seconds total)