Starting phenix.real_space_refine on Fri Mar 6 03:32:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz9_24755/03_2026/7rz9_24755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz9_24755/03_2026/7rz9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rz9_24755/03_2026/7rz9_24755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz9_24755/03_2026/7rz9_24755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rz9_24755/03_2026/7rz9_24755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz9_24755/03_2026/7rz9_24755.map" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27934 Number of models: 1 Model: "" Number of chains: 2 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 Restraints were copied for chains: C, D Time building chain proxies: 13.46, per 1000 atoms: 0.48 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 - 3.00 Amino acid : True - 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: 2.32 Conformation dependent library (CDL) restraints added in 1.3 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: 1.18 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: 5.97 Time building geometry restraints manager: 3.14 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: 0.00 - 2.51: 37568 2.51 - 5.02: 904 5.02 - 7.53: 89 7.53 - 10.04: 17 10.04 - 12.55: 4 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 3.040 nonbonded pdb=" O MET B 33 " pdb=" OG SER B 37 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 375 " pdb=" O ASP B 378 " model vdw 2.265 3.040 nonbonded pdb=" OG SER D 375 " pdb=" O ASP D 378 " model vdw 2.265 3.040 nonbonded pdb=" OE2 GLU C 25 " pdb=" OG1 THR C 281 " model vdw 2.308 3.040 ... (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 Time spend for trying shortcut: 0.05 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: 3.160 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- 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 28548 Z= 0.293 Angle : 0.978 12.546 38602 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 : 3.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG C 308 TYR 0.016 0.002 TYR B 373 PHE 0.031 0.003 PHE A1091 TRP 0.034 0.004 TRP C1032 HIS 0.009 0.003 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00652 (28538) covalent geometry : angle 0.97840 (38582) SS BOND : bond 0.00376 ( 10) SS BOND : angle 1.14697 ( 20) hydrogen bonds : bond 0.29644 ( 1155) hydrogen bonds : angle 10.00437 ( 3381) *********************** 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 to be fit. rotamer outliers: 8 poor density : 882 time to evaluate : 1.137 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: 0.7925 (t) cc_final: 0.7700 (t) REVERT: B 533 TYR cc_start: 0.7972 (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: 0.7865 (m-30) REVERT: D 533 TYR cc_start: 0.7813 (t80) cc_final: 0.7498 (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: 0.2006 time to fit residues: 279.0867 Evaluate side-chains 499 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 496 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 359 ASN A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A1037 GLN B 147 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 147 GLN C 359 ASN C 569 ASN C 619 ASN C 714 GLN C1037 GLN D 202 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118367 restraints weight = 44551.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118894 restraints weight = 79657.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119996 restraints weight = 67145.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120794 restraints weight = 43964.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121463 restraints weight = 37914.949| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28548 Z= 0.186 Angle : 0.617 6.214 38602 Z= 0.334 Chirality : 0.043 0.177 4290 Planarity : 0.005 0.076 4866 Dihedral : 5.421 45.297 3842 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.12), residues: 3526 helix: -1.84 (0.10), residues: 1682 sheet: -1.64 (0.25), residues: 372 loop : -1.92 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 628 TYR 0.018 0.002 TYR A 702 PHE 0.022 0.002 PHE A1217 TRP 0.025 0.002 TRP C 323 HIS 0.007 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00423 (28538) covalent geometry : angle 0.61692 (38582) SS BOND : bond 0.00477 ( 10) SS BOND : angle 0.87867 ( 20) hydrogen bonds : bond 0.04694 ( 1155) hydrogen bonds : angle 4.91344 ( 3381) *********************** 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 644 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 642 time to evaluate : 1.050 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: 0.8200 (pt) cc_final: 0.7594 (pt) REVERT: A 60 ASN cc_start: 0.8391 (m-40) cc_final: 0.7873 (t0) REVERT: A 71 TYR cc_start: 0.7046 (m-80) cc_final: 0.6669 (m-80) REVERT: A 186 LEU cc_start: 0.8352 (mp) cc_final: 0.8063 (tp) REVERT: A 363 LEU cc_start: 0.8618 (tp) cc_final: 0.8354 (tt) REVERT: A 425 CYS cc_start: 0.8495 (m) cc_final: 0.8105 (m) REVERT: A 476 ILE cc_start: 0.9118 (mt) cc_final: 0.8357 (mt) REVERT: A 516 SER cc_start: 0.8736 (t) cc_final: 0.8191 (t) REVERT: A 519 ASP cc_start: 0.8602 (m-30) cc_final: 0.8347 (m-30) REVERT: A 627 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 1172 LEU cc_start: 0.7562 (mt) cc_final: 0.7220 (mt) REVERT: A 1220 CYS cc_start: 0.8508 (m) cc_final: 0.8235 (m) REVERT: B 25 GLU cc_start: 0.8309 (mp0) cc_final: 0.7941 (mp0) REVERT: B 86 THR cc_start: 0.9179 (p) cc_final: 0.8912 (t) REVERT: B 168 ILE cc_start: 0.8416 (mm) cc_final: 0.8184 (mm) REVERT: B 185 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6965 (tp30) REVERT: B 298 ASN cc_start: 0.8026 (m-40) cc_final: 0.7824 (m-40) REVERT: B 402 GLU cc_start: 0.7453 (tp30) cc_final: 0.7189 (tm-30) REVERT: B 587 GLN cc_start: 0.8499 (mm-40) cc_final: 0.7759 (mp10) REVERT: B 590 ASP cc_start: 0.6407 (p0) cc_final: 0.6204 (t0) REVERT: B 628 ARG cc_start: 0.6715 (mtm110) cc_final: 0.6247 (ptt180) REVERT: B 647 TYR cc_start: 0.8412 (p90) cc_final: 0.8204 (p90) REVERT: B 789 LEU cc_start: 0.9053 (tp) cc_final: 0.8296 (tp) REVERT: C 87 SER cc_start: 0.9042 (t) cc_final: 0.8777 (t) REVERT: C 138 ASP cc_start: 0.8329 (t70) cc_final: 0.7928 (p0) REVERT: C 186 LEU cc_start: 0.8293 (mp) cc_final: 0.8029 (tp) REVERT: C 209 ILE cc_start: 0.8711 (mm) cc_final: 0.8489 (mt) REVERT: C 262 TRP cc_start: 0.8601 (t-100) cc_final: 0.8257 (t-100) REVERT: C 363 LEU cc_start: 0.8611 (tp) cc_final: 0.8294 (tt) REVERT: C 425 CYS cc_start: 0.8569 (m) cc_final: 0.8200 (m) REVERT: C 476 ILE cc_start: 0.9203 (mt) cc_final: 0.8507 (mt) REVERT: C 587 GLN cc_start: 0.7790 (mm110) cc_final: 0.7156 (mp10) REVERT: C 638 ASP cc_start: 0.7368 (m-30) cc_final: 0.7050 (m-30) REVERT: C 752 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8124 (mttp) REVERT: C 1113 PHE cc_start: 0.6002 (t80) cc_final: 0.5565 (t80) REVERT: C 1178 MET cc_start: 0.8244 (ttp) cc_final: 0.8001 (tmm) REVERT: C 1220 CYS cc_start: 0.8124 (m) cc_final: 0.7852 (m) REVERT: D 25 GLU cc_start: 0.8239 (mp0) cc_final: 0.7899 (mp0) REVERT: D 43 LEU cc_start: 0.7738 (mp) cc_final: 0.7522 (mp) REVERT: D 50 LEU cc_start: 0.8421 (pt) cc_final: 0.8032 (pp) REVERT: D 185 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6892 (tp30) REVERT: D 287 ASP cc_start: 0.8614 (m-30) cc_final: 0.8242 (m-30) REVERT: D 298 ASN cc_start: 0.8134 (m-40) cc_final: 0.7843 (m-40) REVERT: D 574 PHE cc_start: 0.7848 (t80) cc_final: 0.7623 (t80) REVERT: D 789 LEU cc_start: 0.9022 (tp) cc_final: 0.8427 (tp) outliers start: 2 outliers final: 0 residues processed: 644 average time/residue: 0.1794 time to fit residues: 186.7122 Evaluate side-chains 433 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 315 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 278 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 355 ASN C 619 ASN D 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116872 restraints weight = 44983.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118631 restraints weight = 82734.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119492 restraints weight = 55982.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119609 restraints weight = 40239.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121131 restraints weight = 34880.575| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28548 Z= 0.168 Angle : 0.565 6.391 38602 Z= 0.301 Chirality : 0.042 0.147 4290 Planarity : 0.004 0.067 4866 Dihedral : 4.989 43.271 3842 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3526 helix: -0.55 (0.12), residues: 1692 sheet: -1.43 (0.25), residues: 400 loop : -1.73 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 628 TYR 0.015 0.002 TYR B 533 PHE 0.021 0.002 PHE A 101 TRP 0.027 0.001 TRP C 323 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00387 (28538) covalent geometry : angle 0.56533 (38582) SS BOND : bond 0.00446 ( 10) SS BOND : angle 0.74786 ( 20) hydrogen bonds : bond 0.03776 ( 1155) hydrogen bonds : angle 4.38700 ( 3381) *********************** 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 559 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8316 (m-40) cc_final: 0.7984 (t0) REVERT: A 71 TYR cc_start: 0.6987 (m-80) cc_final: 0.6728 (m-80) REVERT: A 101 PHE cc_start: 0.8800 (p90) cc_final: 0.8536 (p90) REVERT: A 138 ASP cc_start: 0.8150 (t70) cc_final: 0.7730 (p0) REVERT: A 186 LEU cc_start: 0.8366 (mp) cc_final: 0.7802 (tp) REVERT: A 209 ILE cc_start: 0.8792 (mm) cc_final: 0.8557 (mt) REVERT: A 362 GLU cc_start: 0.8249 (tt0) cc_final: 0.8035 (tt0) REVERT: A 425 CYS cc_start: 0.8465 (m) cc_final: 0.8216 (m) REVERT: A 476 ILE cc_start: 0.9210 (mt) cc_final: 0.8508 (mt) REVERT: A 503 MET cc_start: 0.8149 (ttm) cc_final: 0.7842 (ttp) REVERT: A 627 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 1113 PHE cc_start: 0.6243 (t80) cc_final: 0.5715 (t80) REVERT: A 1172 LEU cc_start: 0.7762 (mt) cc_final: 0.7317 (mt) REVERT: A 1220 CYS cc_start: 0.8452 (m) cc_final: 0.8195 (m) REVERT: B 25 GLU cc_start: 0.8393 (mp0) cc_final: 0.7939 (mp0) REVERT: B 86 THR cc_start: 0.9206 (p) cc_final: 0.8920 (t) REVERT: B 185 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6907 (tp30) REVERT: B 419 GLU cc_start: 0.7170 (tp30) cc_final: 0.6961 (tp30) REVERT: B 587 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7755 (mp10) REVERT: B 599 ARG cc_start: 0.8454 (mtt180) cc_final: 0.7911 (ttm170) REVERT: B 789 LEU cc_start: 0.9124 (tp) cc_final: 0.8339 (tp) REVERT: C 138 ASP cc_start: 0.8294 (t70) cc_final: 0.7890 (p0) REVERT: C 186 LEU cc_start: 0.8308 (mp) cc_final: 0.7769 (tp) REVERT: C 363 LEU cc_start: 0.8601 (tp) cc_final: 0.8337 (tt) REVERT: C 476 ILE cc_start: 0.9210 (mt) cc_final: 0.8562 (mt) REVERT: C 606 TRP cc_start: 0.8247 (m-10) cc_final: 0.7892 (m-10) REVERT: C 638 ASP cc_start: 0.7584 (m-30) cc_final: 0.7032 (m-30) REVERT: C 752 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8008 (mttt) REVERT: C 1016 ASN cc_start: 0.7827 (t0) cc_final: 0.7585 (t0) REVERT: C 1113 PHE cc_start: 0.5923 (t80) cc_final: 0.5612 (t80) REVERT: C 1220 CYS cc_start: 0.8018 (m) cc_final: 0.7818 (m) REVERT: D 25 GLU cc_start: 0.8170 (mp0) cc_final: 0.7841 (mp0) REVERT: D 287 ASP cc_start: 0.8681 (m-30) cc_final: 0.8333 (m-30) REVERT: D 298 ASN cc_start: 0.8094 (m-40) cc_final: 0.7829 (t0) REVERT: D 402 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6544 (tm-30) REVERT: D 481 ILE cc_start: 0.9415 (mt) cc_final: 0.8937 (pt) REVERT: D 628 ARG cc_start: 0.6785 (mtm110) cc_final: 0.5739 (ptp-170) REVERT: D 642 GLN cc_start: 0.5321 (pp30) cc_final: 0.5020 (pp30) REVERT: D 789 LEU cc_start: 0.9053 (tp) cc_final: 0.8458 (tp) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1777 time to fit residues: 162.4524 Evaluate side-chains 415 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 322 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 333 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 355 ASN D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115298 restraints weight = 44878.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117662 restraints weight = 81401.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118238 restraints weight = 55909.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118838 restraints weight = 38380.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119483 restraints weight = 33334.073| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28548 Z= 0.167 Angle : 0.552 6.917 38602 Z= 0.292 Chirality : 0.043 0.277 4290 Planarity : 0.004 0.063 4866 Dihedral : 4.807 41.283 3842 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3526 helix: 0.12 (0.13), residues: 1676 sheet: -1.63 (0.25), residues: 424 loop : -1.49 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 628 TYR 0.019 0.001 TYR D 533 PHE 0.023 0.002 PHE C 101 TRP 0.031 0.001 TRP C 323 HIS 0.007 0.001 HIS C1092 Details of bonding type rmsd covalent geometry : bond 0.00386 (28538) covalent geometry : angle 0.55182 (38582) SS BOND : bond 0.00267 ( 10) SS BOND : angle 0.59959 ( 20) hydrogen bonds : bond 0.03466 ( 1155) hydrogen bonds : angle 4.16975 ( 3381) *********************** 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 539 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6970 (m-80) cc_final: 0.6701 (m-80) REVERT: A 138 ASP cc_start: 0.8097 (t70) cc_final: 0.7708 (p0) REVERT: A 186 LEU cc_start: 0.8459 (mp) cc_final: 0.7912 (tp) REVERT: A 209 ILE cc_start: 0.8756 (mm) cc_final: 0.8482 (mt) REVERT: A 425 CYS cc_start: 0.8408 (m) cc_final: 0.8148 (m) REVERT: A 476 ILE cc_start: 0.9263 (mt) cc_final: 0.8515 (mt) REVERT: A 569 ASN cc_start: 0.7410 (t0) cc_final: 0.6763 (p0) REVERT: A 627 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 1113 PHE cc_start: 0.6199 (t80) cc_final: 0.5674 (t80) REVERT: A 1172 LEU cc_start: 0.7954 (mt) cc_final: 0.7558 (mt) REVERT: A 1220 CYS cc_start: 0.8353 (m) cc_final: 0.8098 (m) REVERT: B 25 GLU cc_start: 0.8410 (mp0) cc_final: 0.7920 (mp0) REVERT: B 43 LEU cc_start: 0.7296 (mp) cc_final: 0.7063 (mp) REVERT: B 86 THR cc_start: 0.9170 (p) cc_final: 0.8906 (t) REVERT: B 334 LYS cc_start: 0.7774 (mptt) cc_final: 0.7573 (mmtp) REVERT: B 516 SER cc_start: 0.8338 (t) cc_final: 0.8110 (t) REVERT: B 533 TYR cc_start: 0.8126 (t80) cc_final: 0.7855 (t80) REVERT: B 599 ARG cc_start: 0.8458 (mtt180) cc_final: 0.7875 (ttm170) REVERT: B 628 ARG cc_start: 0.6970 (mtm110) cc_final: 0.6665 (mtm180) REVERT: B 789 LEU cc_start: 0.9083 (tp) cc_final: 0.8394 (tp) REVERT: C 138 ASP cc_start: 0.8266 (t70) cc_final: 0.7822 (p0) REVERT: C 157 LYS cc_start: 0.7924 (tptt) cc_final: 0.7627 (tptm) REVERT: C 186 LEU cc_start: 0.8300 (mp) cc_final: 0.7827 (tp) REVERT: C 209 ILE cc_start: 0.8737 (mm) cc_final: 0.8433 (mt) REVERT: C 363 LEU cc_start: 0.8607 (tp) cc_final: 0.8338 (tt) REVERT: C 476 ILE cc_start: 0.9351 (mt) cc_final: 0.8698 (mt) REVERT: C 638 ASP cc_start: 0.7751 (m-30) cc_final: 0.7171 (m-30) REVERT: C 752 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8017 (mttt) REVERT: C 1016 ASN cc_start: 0.7930 (t0) cc_final: 0.7727 (t0) REVERT: C 1113 PHE cc_start: 0.6022 (t80) cc_final: 0.5629 (t80) REVERT: D 25 GLU cc_start: 0.8268 (mp0) cc_final: 0.7938 (mp0) REVERT: D 43 LEU cc_start: 0.7224 (mp) cc_final: 0.6915 (mp) REVERT: D 287 ASP cc_start: 0.8686 (m-30) cc_final: 0.8197 (m-30) REVERT: D 298 ASN cc_start: 0.8118 (m-40) cc_final: 0.7888 (m-40) REVERT: D 422 GLU cc_start: 0.7090 (pm20) cc_final: 0.6721 (pm20) REVERT: D 481 ILE cc_start: 0.9396 (mt) cc_final: 0.8937 (pt) REVERT: D 587 GLN cc_start: 0.8498 (mm110) cc_final: 0.8268 (mm110) REVERT: D 789 LEU cc_start: 0.9112 (tp) cc_final: 0.8697 (tp) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.1752 time to fit residues: 154.9090 Evaluate side-chains 408 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 317 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 243 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 321 optimal weight: 0.2980 chunk 177 optimal weight: 10.0000 chunk 227 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 147 GLN A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 224 ASN C 355 ASN C 619 ASN D 147 GLN D 435 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130987 restraints weight = 43079.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131012 restraints weight = 78334.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132186 restraints weight = 65853.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132360 restraints weight = 42568.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133195 restraints weight = 39380.355| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28548 Z= 0.100 Angle : 0.496 6.764 38602 Z= 0.261 Chirality : 0.040 0.201 4290 Planarity : 0.004 0.057 4866 Dihedral : 4.431 37.502 3842 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3526 helix: 0.70 (0.13), residues: 1664 sheet: -1.62 (0.24), residues: 432 loop : -1.26 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 42 TYR 0.015 0.001 TYR C 77 PHE 0.023 0.001 PHE A 101 TRP 0.033 0.001 TRP C 323 HIS 0.006 0.001 HIS C1092 Details of bonding type rmsd covalent geometry : bond 0.00226 (28538) covalent geometry : angle 0.49519 (38582) SS BOND : bond 0.00216 ( 10) SS BOND : angle 1.03840 ( 20) hydrogen bonds : bond 0.02979 ( 1155) hydrogen bonds : angle 3.80379 ( 3381) *********************** 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 566 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6772 (m-80) cc_final: 0.6519 (m-80) REVERT: A 138 ASP cc_start: 0.7996 (t70) cc_final: 0.7708 (p0) REVERT: A 186 LEU cc_start: 0.8272 (mp) cc_final: 0.7824 (tp) REVERT: A 425 CYS cc_start: 0.8262 (m) cc_final: 0.7995 (m) REVERT: A 476 ILE cc_start: 0.9004 (mt) cc_final: 0.8289 (mt) REVERT: A 503 MET cc_start: 0.7713 (ttp) cc_final: 0.7350 (ttp) REVERT: A 516 SER cc_start: 0.8779 (t) cc_final: 0.8497 (t) REVERT: A 517 PHE cc_start: 0.9146 (p90) cc_final: 0.8943 (p90) REVERT: A 569 ASN cc_start: 0.7238 (t0) cc_final: 0.6592 (p0) REVERT: A 811 LEU cc_start: 0.8322 (tt) cc_final: 0.7873 (mt) REVERT: A 1113 PHE cc_start: 0.6045 (t80) cc_final: 0.5613 (t80) REVERT: B 25 GLU cc_start: 0.8248 (mp0) cc_final: 0.7782 (mp0) REVERT: B 43 LEU cc_start: 0.7118 (mp) cc_final: 0.6904 (mp) REVERT: B 86 THR cc_start: 0.9152 (p) cc_final: 0.8905 (t) REVERT: B 334 LYS cc_start: 0.7550 (mmtp) cc_final: 0.7200 (mmtp) REVERT: B 419 GLU cc_start: 0.7084 (tp30) cc_final: 0.6839 (tp30) REVERT: B 463 MET cc_start: 0.7511 (mtp) cc_final: 0.7287 (mtm) REVERT: B 516 SER cc_start: 0.8295 (t) cc_final: 0.8085 (t) REVERT: B 518 LEU cc_start: 0.8673 (pp) cc_final: 0.8222 (pp) REVERT: B 599 ARG cc_start: 0.8528 (mtt180) cc_final: 0.7900 (ttm170) REVERT: B 647 TYR cc_start: 0.8361 (p90) cc_final: 0.7911 (p90) REVERT: B 789 LEU cc_start: 0.8983 (tp) cc_final: 0.8314 (tp) REVERT: C 101 PHE cc_start: 0.8698 (p90) cc_final: 0.8482 (p90) REVERT: C 138 ASP cc_start: 0.8150 (t70) cc_final: 0.7829 (p0) REVERT: C 157 LYS cc_start: 0.7779 (tptt) cc_final: 0.7469 (tptm) REVERT: C 186 LEU cc_start: 0.8270 (mp) cc_final: 0.7865 (tp) REVERT: C 363 LEU cc_start: 0.8644 (tp) cc_final: 0.8419 (tt) REVERT: C 476 ILE cc_start: 0.9132 (mt) cc_final: 0.8454 (mt) REVERT: C 752 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8007 (mttt) REVERT: C 1113 PHE cc_start: 0.5765 (t80) cc_final: 0.5404 (t80) REVERT: C 1126 TRP cc_start: 0.6995 (m100) cc_final: 0.5432 (t60) REVERT: C 1172 LEU cc_start: 0.8282 (mt) cc_final: 0.7841 (mt) REVERT: D 25 GLU cc_start: 0.8162 (mp0) cc_final: 0.7859 (mp0) REVERT: D 287 ASP cc_start: 0.8545 (m-30) cc_final: 0.8334 (m-30) REVERT: D 518 LEU cc_start: 0.8712 (pp) cc_final: 0.8351 (pp) REVERT: D 587 GLN cc_start: 0.8355 (mm110) cc_final: 0.8154 (mm110) REVERT: D 789 LEU cc_start: 0.9120 (tp) cc_final: 0.8604 (tp) outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 0.1820 time to fit residues: 167.9732 Evaluate side-chains 417 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 113 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 355 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121130 restraints weight = 44076.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123135 restraints weight = 77818.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123214 restraints weight = 41967.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123267 restraints weight = 34669.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123627 restraints weight = 31081.842| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28548 Z= 0.149 Angle : 0.531 6.613 38602 Z= 0.279 Chirality : 0.042 0.204 4290 Planarity : 0.004 0.060 4866 Dihedral : 4.459 34.823 3842 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3526 helix: 0.79 (0.13), residues: 1678 sheet: -1.54 (0.25), residues: 426 loop : -1.19 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.020 0.001 TYR B 533 PHE 0.023 0.002 PHE A1217 TRP 0.031 0.001 TRP C 323 HIS 0.007 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00346 (28538) covalent geometry : angle 0.53062 (38582) SS BOND : bond 0.00311 ( 10) SS BOND : angle 1.12037 ( 20) hydrogen bonds : bond 0.03197 ( 1155) hydrogen bonds : angle 3.90298 ( 3381) *********************** 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 537 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6747 (m-80) cc_final: 0.6464 (m-80) REVERT: A 138 ASP cc_start: 0.8049 (t70) cc_final: 0.7689 (p0) REVERT: A 186 LEU cc_start: 0.8314 (mp) cc_final: 0.7788 (tp) REVERT: A 209 ILE cc_start: 0.8763 (mm) cc_final: 0.8423 (mt) REVERT: A 355 ASN cc_start: 0.6494 (m-40) cc_final: 0.6165 (t0) REVERT: A 425 CYS cc_start: 0.8233 (m) cc_final: 0.8006 (m) REVERT: A 476 ILE cc_start: 0.9221 (mt) cc_final: 0.8594 (mt) REVERT: A 569 ASN cc_start: 0.7277 (t0) cc_final: 0.6537 (p0) REVERT: A 811 LEU cc_start: 0.8399 (tt) cc_final: 0.7963 (mt) REVERT: A 813 GLU cc_start: 0.6335 (tt0) cc_final: 0.5603 (tm-30) REVERT: A 1113 PHE cc_start: 0.6082 (t80) cc_final: 0.5553 (t80) REVERT: B 25 GLU cc_start: 0.8330 (mp0) cc_final: 0.7879 (mp0) REVERT: B 86 THR cc_start: 0.9165 (p) cc_final: 0.8838 (t) REVERT: B 330 GLU cc_start: 0.7850 (tt0) cc_final: 0.7635 (tt0) REVERT: B 419 GLU cc_start: 0.7071 (tp30) cc_final: 0.6789 (tp30) REVERT: B 516 SER cc_start: 0.8353 (t) cc_final: 0.8077 (t) REVERT: B 518 LEU cc_start: 0.8776 (pp) cc_final: 0.8276 (pp) REVERT: B 599 ARG cc_start: 0.8465 (mtt180) cc_final: 0.7848 (ttm170) REVERT: B 789 LEU cc_start: 0.9027 (tp) cc_final: 0.8347 (tp) REVERT: C 60 ASN cc_start: 0.8305 (m-40) cc_final: 0.7891 (t0) REVERT: C 71 TYR cc_start: 0.7173 (m-10) cc_final: 0.6762 (m-80) REVERT: C 138 ASP cc_start: 0.8159 (t70) cc_final: 0.7749 (p0) REVERT: C 157 LYS cc_start: 0.7691 (tptt) cc_final: 0.7404 (tptm) REVERT: C 186 LEU cc_start: 0.8338 (mp) cc_final: 0.7871 (tp) REVERT: C 209 ILE cc_start: 0.8670 (mm) cc_final: 0.8283 (mt) REVERT: C 325 GLN cc_start: 0.5523 (tp-100) cc_final: 0.5181 (tp-100) REVERT: C 363 LEU cc_start: 0.8614 (tp) cc_final: 0.8354 (tt) REVERT: C 414 MET cc_start: 0.5401 (ttm) cc_final: 0.4942 (tpp) REVERT: C 476 ILE cc_start: 0.9305 (mt) cc_final: 0.8683 (mt) REVERT: C 752 LYS cc_start: 0.8660 (tttt) cc_final: 0.8381 (mttt) REVERT: C 1113 PHE cc_start: 0.5888 (t80) cc_final: 0.5620 (t80) REVERT: C 1172 LEU cc_start: 0.8246 (mt) cc_final: 0.7936 (mt) REVERT: D 25 GLU cc_start: 0.8219 (mp0) cc_final: 0.7806 (mp0) REVERT: D 287 ASP cc_start: 0.8613 (m-30) cc_final: 0.8312 (m-30) REVERT: D 518 LEU cc_start: 0.8804 (pp) cc_final: 0.8485 (pp) REVERT: D 587 GLN cc_start: 0.8445 (mm110) cc_final: 0.8075 (mm110) REVERT: D 789 LEU cc_start: 0.9051 (tp) cc_final: 0.8601 (tp) outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.1678 time to fit residues: 150.0736 Evaluate side-chains 416 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 166 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 281 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 219 HIS C 355 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 435 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120171 restraints weight = 43806.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121836 restraints weight = 81186.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122376 restraints weight = 45119.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122324 restraints weight = 36219.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122672 restraints weight = 32480.519| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28548 Z= 0.168 Angle : 0.552 7.896 38602 Z= 0.290 Chirality : 0.043 0.177 4290 Planarity : 0.004 0.062 4866 Dihedral : 4.523 32.140 3842 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3526 helix: 0.86 (0.13), residues: 1674 sheet: -1.69 (0.25), residues: 416 loop : -1.21 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.020 0.001 TYR B 533 PHE 0.025 0.002 PHE C1217 TRP 0.031 0.001 TRP C 323 HIS 0.006 0.001 HIS C1092 Details of bonding type rmsd covalent geometry : bond 0.00390 (28538) covalent geometry : angle 0.55141 (38582) SS BOND : bond 0.00336 ( 10) SS BOND : angle 0.98386 ( 20) hydrogen bonds : bond 0.03281 ( 1155) hydrogen bonds : angle 3.98348 ( 3381) *********************** 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 527 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6844 (m-80) cc_final: 0.6564 (m-80) REVERT: A 138 ASP cc_start: 0.8176 (t70) cc_final: 0.7945 (p0) REVERT: A 186 LEU cc_start: 0.8168 (mp) cc_final: 0.7584 (tp) REVERT: A 425 CYS cc_start: 0.8235 (m) cc_final: 0.8034 (m) REVERT: A 476 ILE cc_start: 0.9205 (mt) cc_final: 0.8536 (mt) REVERT: A 569 ASN cc_start: 0.7336 (t0) cc_final: 0.6567 (p0) REVERT: A 811 LEU cc_start: 0.8403 (tt) cc_final: 0.7914 (mt) REVERT: A 1113 PHE cc_start: 0.6014 (t80) cc_final: 0.5587 (t80) REVERT: A 1217 PHE cc_start: 0.7898 (t80) cc_final: 0.7536 (t80) REVERT: A 1220 CYS cc_start: 0.8180 (m) cc_final: 0.7929 (m) REVERT: B 25 GLU cc_start: 0.8333 (mp0) cc_final: 0.7844 (mp0) REVERT: B 86 THR cc_start: 0.9155 (p) cc_final: 0.8926 (t) REVERT: B 516 SER cc_start: 0.8333 (t) cc_final: 0.8114 (t) REVERT: B 518 LEU cc_start: 0.8767 (pp) cc_final: 0.8396 (pp) REVERT: B 578 TRP cc_start: 0.8971 (t-100) cc_final: 0.8561 (t-100) REVERT: B 789 LEU cc_start: 0.9016 (tp) cc_final: 0.8338 (tp) REVERT: C 60 ASN cc_start: 0.8268 (m-40) cc_final: 0.7923 (t0) REVERT: C 138 ASP cc_start: 0.8133 (t70) cc_final: 0.7716 (p0) REVERT: C 157 LYS cc_start: 0.7728 (tptt) cc_final: 0.7432 (tptm) REVERT: C 186 LEU cc_start: 0.8147 (mp) cc_final: 0.7696 (tp) REVERT: C 209 ILE cc_start: 0.8588 (mm) cc_final: 0.8196 (mt) REVERT: C 363 LEU cc_start: 0.8576 (tp) cc_final: 0.8321 (tt) REVERT: C 476 ILE cc_start: 0.9278 (mt) cc_final: 0.8629 (mt) REVERT: C 752 LYS cc_start: 0.8656 (tttt) cc_final: 0.8301 (mttt) REVERT: C 1113 PHE cc_start: 0.6034 (t80) cc_final: 0.5634 (t80) REVERT: C 1172 LEU cc_start: 0.8351 (mt) cc_final: 0.8084 (mt) REVERT: D 25 GLU cc_start: 0.8262 (mp0) cc_final: 0.7850 (mp0) REVERT: D 287 ASP cc_start: 0.8626 (m-30) cc_final: 0.8380 (m-30) REVERT: D 431 GLU cc_start: 0.6616 (tp30) cc_final: 0.6099 (tp30) REVERT: D 518 LEU cc_start: 0.8778 (pp) cc_final: 0.8411 (pp) REVERT: D 789 LEU cc_start: 0.9027 (tp) cc_final: 0.8565 (tp) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.1663 time to fit residues: 145.3585 Evaluate side-chains 406 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 308 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 435 HIS C 355 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116244 restraints weight = 44421.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117667 restraints weight = 83048.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118561 restraints weight = 60233.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118757 restraints weight = 41670.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119689 restraints weight = 36711.443| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28548 Z= 0.165 Angle : 0.555 9.029 38602 Z= 0.292 Chirality : 0.043 0.190 4290 Planarity : 0.004 0.062 4866 Dihedral : 4.562 31.517 3842 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3526 helix: 0.85 (0.13), residues: 1684 sheet: -1.75 (0.25), residues: 416 loop : -1.20 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 599 TYR 0.022 0.001 TYR D 533 PHE 0.017 0.002 PHE B 74 TRP 0.035 0.002 TRP C 323 HIS 0.007 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00385 (28538) covalent geometry : angle 0.55524 (38582) SS BOND : bond 0.00247 ( 10) SS BOND : angle 0.86066 ( 20) hydrogen bonds : bond 0.03262 ( 1155) hydrogen bonds : angle 3.98042 ( 3381) *********************** 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 518 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6961 (m-80) cc_final: 0.6654 (m-80) REVERT: A 138 ASP cc_start: 0.8217 (t70) cc_final: 0.7934 (p0) REVERT: A 186 LEU cc_start: 0.8228 (mp) cc_final: 0.7688 (tp) REVERT: A 209 ILE cc_start: 0.8682 (mm) cc_final: 0.8329 (mt) REVERT: A 425 CYS cc_start: 0.8308 (m) cc_final: 0.8098 (m) REVERT: A 476 ILE cc_start: 0.9238 (mt) cc_final: 0.8549 (mt) REVERT: A 569 ASN cc_start: 0.7364 (t0) cc_final: 0.6506 (p0) REVERT: A 811 LEU cc_start: 0.8347 (tt) cc_final: 0.7876 (mt) REVERT: A 1113 PHE cc_start: 0.6140 (t80) cc_final: 0.5668 (t80) REVERT: A 1217 PHE cc_start: 0.7980 (t80) cc_final: 0.7679 (t80) REVERT: A 1220 CYS cc_start: 0.8204 (m) cc_final: 0.8001 (m) REVERT: B 86 THR cc_start: 0.9154 (p) cc_final: 0.8946 (t) REVERT: B 334 LYS cc_start: 0.7745 (mptt) cc_final: 0.7526 (mmtp) REVERT: B 419 GLU cc_start: 0.7145 (tp30) cc_final: 0.6877 (tp30) REVERT: B 516 SER cc_start: 0.8327 (t) cc_final: 0.8119 (t) REVERT: B 518 LEU cc_start: 0.8776 (pp) cc_final: 0.8460 (pp) REVERT: B 578 TRP cc_start: 0.8961 (t-100) cc_final: 0.8545 (t-100) REVERT: B 789 LEU cc_start: 0.9000 (tp) cc_final: 0.8383 (tp) REVERT: C 138 ASP cc_start: 0.8139 (t70) cc_final: 0.7697 (p0) REVERT: C 157 LYS cc_start: 0.7790 (tptt) cc_final: 0.7481 (tptm) REVERT: C 186 LEU cc_start: 0.8297 (mp) cc_final: 0.7705 (tp) REVERT: C 209 ILE cc_start: 0.8539 (mm) cc_final: 0.8165 (mt) REVERT: C 363 LEU cc_start: 0.8598 (tp) cc_final: 0.8295 (tt) REVERT: C 476 ILE cc_start: 0.9309 (mt) cc_final: 0.8607 (mt) REVERT: C 752 LYS cc_start: 0.8703 (tttt) cc_final: 0.8269 (mttt) REVERT: C 1113 PHE cc_start: 0.6207 (t80) cc_final: 0.5718 (t80) REVERT: C 1217 PHE cc_start: 0.7874 (t80) cc_final: 0.7662 (t80) REVERT: D 25 GLU cc_start: 0.8318 (mp0) cc_final: 0.7872 (mp0) REVERT: D 168 ILE cc_start: 0.8563 (mm) cc_final: 0.8337 (mm) REVERT: D 189 GLU cc_start: 0.7517 (tp30) cc_final: 0.7305 (tp30) REVERT: D 287 ASP cc_start: 0.8735 (m-30) cc_final: 0.8459 (m-30) REVERT: D 501 SER cc_start: 0.9066 (p) cc_final: 0.8852 (t) REVERT: D 789 LEU cc_start: 0.8990 (tp) cc_final: 0.8583 (tp) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.1746 time to fit residues: 149.6072 Evaluate side-chains 413 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 224 optimal weight: 0.9980 chunk 243 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 147 GLN C 355 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127760 restraints weight = 42889.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128634 restraints weight = 76159.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129608 restraints weight = 55508.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129506 restraints weight = 40432.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130090 restraints weight = 36316.205| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28548 Z= 0.115 Angle : 0.525 8.476 38602 Z= 0.274 Chirality : 0.041 0.158 4290 Planarity : 0.004 0.059 4866 Dihedral : 4.381 29.223 3842 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3526 helix: 1.01 (0.13), residues: 1686 sheet: -1.74 (0.24), residues: 426 loop : -1.16 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 599 TYR 0.022 0.001 TYR D 533 PHE 0.029 0.001 PHE B 109 TRP 0.036 0.001 TRP C 323 HIS 0.005 0.001 HIS C1092 Details of bonding type rmsd covalent geometry : bond 0.00266 (28538) covalent geometry : angle 0.52459 (38582) SS BOND : bond 0.00203 ( 10) SS BOND : angle 0.74934 ( 20) hydrogen bonds : bond 0.03020 ( 1155) hydrogen bonds : angle 3.81563 ( 3381) *********************** 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 517 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6783 (m-80) cc_final: 0.6458 (m-80) REVERT: A 186 LEU cc_start: 0.8194 (mp) cc_final: 0.7674 (tp) REVERT: A 209 ILE cc_start: 0.8594 (mm) cc_final: 0.8203 (mt) REVERT: A 425 CYS cc_start: 0.8242 (m) cc_final: 0.7984 (m) REVERT: A 476 ILE cc_start: 0.9224 (mt) cc_final: 0.8548 (mt) REVERT: A 569 ASN cc_start: 0.7176 (t0) cc_final: 0.6453 (p0) REVERT: A 811 LEU cc_start: 0.8377 (tt) cc_final: 0.7916 (mt) REVERT: A 1113 PHE cc_start: 0.5896 (t80) cc_final: 0.5512 (t80) REVERT: A 1182 MET cc_start: 0.8145 (mmp) cc_final: 0.7859 (mmp) REVERT: A 1217 PHE cc_start: 0.7825 (t80) cc_final: 0.7541 (t80) REVERT: B 25 GLU cc_start: 0.8277 (mp0) cc_final: 0.7798 (pm20) REVERT: B 86 THR cc_start: 0.9103 (p) cc_final: 0.8870 (t) REVERT: B 298 ASN cc_start: 0.7640 (m-40) cc_final: 0.7428 (m-40) REVERT: B 419 GLU cc_start: 0.7035 (tp30) cc_final: 0.6781 (tp30) REVERT: B 518 LEU cc_start: 0.8693 (pp) cc_final: 0.8349 (pp) REVERT: B 578 TRP cc_start: 0.8956 (t-100) cc_final: 0.8518 (t-100) REVERT: B 789 LEU cc_start: 0.8968 (tp) cc_final: 0.8032 (tp) REVERT: C 71 TYR cc_start: 0.7105 (m-10) cc_final: 0.6661 (m-80) REVERT: C 138 ASP cc_start: 0.8040 (t70) cc_final: 0.7691 (p0) REVERT: C 157 LYS cc_start: 0.7676 (tptt) cc_final: 0.7416 (tptm) REVERT: C 186 LEU cc_start: 0.8194 (mp) cc_final: 0.7683 (tp) REVERT: C 363 LEU cc_start: 0.8620 (tp) cc_final: 0.8356 (tt) REVERT: C 476 ILE cc_start: 0.9304 (mt) cc_final: 0.8627 (mt) REVERT: C 752 LYS cc_start: 0.8630 (tttt) cc_final: 0.8296 (mttt) REVERT: C 1113 PHE cc_start: 0.5907 (t80) cc_final: 0.5574 (t80) REVERT: C 1217 PHE cc_start: 0.7639 (t80) cc_final: 0.7434 (t80) REVERT: D 25 GLU cc_start: 0.8155 (mp0) cc_final: 0.7768 (mp0) REVERT: D 168 ILE cc_start: 0.8570 (mm) cc_final: 0.8356 (mm) REVERT: D 501 SER cc_start: 0.9077 (p) cc_final: 0.8854 (t) REVERT: D 518 LEU cc_start: 0.8625 (pp) cc_final: 0.8396 (pp) REVERT: D 789 LEU cc_start: 0.8922 (tp) cc_final: 0.8565 (tp) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1718 time to fit residues: 146.4510 Evaluate side-chains 394 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 231 optimal weight: 0.0670 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 183 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 341 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- 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 ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN B 224 ASN C 355 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123876 restraints weight = 43642.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125814 restraints weight = 74952.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125792 restraints weight = 40461.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125890 restraints weight = 34271.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126223 restraints weight = 30385.615| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28548 Z= 0.101 Angle : 0.513 8.452 38602 Z= 0.268 Chirality : 0.041 0.156 4290 Planarity : 0.004 0.056 4866 Dihedral : 4.217 27.271 3842 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3526 helix: 1.14 (0.13), residues: 1682 sheet: -1.63 (0.25), residues: 422 loop : -1.15 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 599 TYR 0.022 0.001 TYR D 533 PHE 0.020 0.001 PHE B 74 TRP 0.037 0.002 TRP C 323 HIS 0.005 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00232 (28538) covalent geometry : angle 0.51332 (38582) SS BOND : bond 0.00210 ( 10) SS BOND : angle 0.75633 ( 20) hydrogen bonds : bond 0.02899 ( 1155) hydrogen bonds : angle 3.74329 ( 3381) ********************** 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 525 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6769 (m-80) cc_final: 0.6457 (m-80) REVERT: A 186 LEU cc_start: 0.8166 (mp) cc_final: 0.7652 (tp) REVERT: A 361 MET cc_start: 0.7649 (mmm) cc_final: 0.7448 (mmm) REVERT: A 425 CYS cc_start: 0.8197 (m) cc_final: 0.7964 (m) REVERT: A 476 ILE cc_start: 0.9054 (mt) cc_final: 0.8351 (mt) REVERT: A 569 ASN cc_start: 0.7087 (t0) cc_final: 0.6366 (p0) REVERT: A 811 LEU cc_start: 0.8355 (tt) cc_final: 0.7903 (mt) REVERT: A 1113 PHE cc_start: 0.5985 (t80) cc_final: 0.5551 (t80) REVERT: A 1126 TRP cc_start: 0.6877 (m100) cc_final: 0.5213 (t60) REVERT: A 1182 MET cc_start: 0.8163 (mmp) cc_final: 0.7959 (mmp) REVERT: A 1217 PHE cc_start: 0.7849 (t80) cc_final: 0.7647 (t80) REVERT: B 25 GLU cc_start: 0.8242 (mp0) cc_final: 0.7846 (pm20) REVERT: B 86 THR cc_start: 0.9109 (p) cc_final: 0.8895 (t) REVERT: B 298 ASN cc_start: 0.7736 (m-40) cc_final: 0.7490 (m-40) REVERT: B 419 GLU cc_start: 0.6997 (tp30) cc_final: 0.6760 (tp30) REVERT: B 518 LEU cc_start: 0.8756 (pp) cc_final: 0.8475 (pp) REVERT: B 578 TRP cc_start: 0.8954 (t-100) cc_final: 0.8435 (t-100) REVERT: B 789 LEU cc_start: 0.8917 (tp) cc_final: 0.7984 (tp) REVERT: C 71 TYR cc_start: 0.7068 (m-10) cc_final: 0.6661 (m-80) REVERT: C 138 ASP cc_start: 0.8073 (t70) cc_final: 0.7708 (p0) REVERT: C 157 LYS cc_start: 0.7626 (tptt) cc_final: 0.7369 (tptm) REVERT: C 186 LEU cc_start: 0.8132 (mp) cc_final: 0.7624 (tp) REVERT: C 209 ILE cc_start: 0.8440 (mm) cc_final: 0.8021 (mt) REVERT: C 363 LEU cc_start: 0.8552 (tp) cc_final: 0.8308 (tt) REVERT: C 425 CYS cc_start: 0.8242 (m) cc_final: 0.8017 (m) REVERT: C 476 ILE cc_start: 0.9159 (mt) cc_final: 0.8485 (mt) REVERT: C 752 LYS cc_start: 0.8695 (tttt) cc_final: 0.8268 (mttt) REVERT: C 1113 PHE cc_start: 0.6031 (t80) cc_final: 0.5563 (t80) REVERT: C 1126 TRP cc_start: 0.7036 (m100) cc_final: 0.5463 (t60) REVERT: D 25 GLU cc_start: 0.8130 (mp0) cc_final: 0.7802 (mp0) REVERT: D 168 ILE cc_start: 0.8540 (mm) cc_final: 0.8323 (mm) REVERT: D 287 ASP cc_start: 0.8644 (m-30) cc_final: 0.8352 (m-30) REVERT: D 518 LEU cc_start: 0.8790 (pp) cc_final: 0.8485 (pp) REVERT: D 752 LYS cc_start: 0.8566 (ttpt) cc_final: 0.7519 (ttpp) REVERT: D 789 LEU cc_start: 0.8856 (tp) cc_final: 0.8308 (tp) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.1665 time to fit residues: 145.6955 Evaluate side-chains 415 residues out of total 3022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 326 optimal weight: 0.4980 chunk 173 optimal weight: 0.0970 chunk 232 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 236 optimal weight: 0.6980 chunk 202 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS C 355 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123474 restraints weight = 43775.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125227 restraints weight = 78917.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126050 restraints weight = 49042.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126051 restraints weight = 36146.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126491 restraints weight = 33697.490| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28548 Z= 0.095 Angle : 0.499 8.314 38602 Z= 0.260 Chirality : 0.040 0.151 4290 Planarity : 0.004 0.055 4866 Dihedral : 4.086 26.903 3842 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3526 helix: 1.25 (0.13), residues: 1690 sheet: -1.63 (0.24), residues: 434 loop : -1.05 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 599 TYR 0.020 0.001 TYR D 533 PHE 0.019 0.001 PHE B 74 TRP 0.035 0.002 TRP D 323 HIS 0.003 0.001 HIS C1092 Details of bonding type rmsd covalent geometry : bond 0.00213 (28538) covalent geometry : angle 0.49845 (38582) SS BOND : bond 0.00176 ( 10) SS BOND : angle 0.72038 ( 20) hydrogen bonds : bond 0.02718 ( 1155) hydrogen bonds : angle 3.62160 ( 3381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.96 seconds wall clock time: 77 minutes 38.32 seconds (4658.32 seconds total)