Starting phenix.real_space_refine on Wed Mar 12 01:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kbx_37086/03_2025/8kbx_37086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kbx_37086/03_2025/8kbx_37086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kbx_37086/03_2025/8kbx_37086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kbx_37086/03_2025/8kbx_37086.map" model { file = "/net/cci-nas-00/data/ceres_data/8kbx_37086/03_2025/8kbx_37086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kbx_37086/03_2025/8kbx_37086.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 15 5.16 5 C 4178 2.51 5 N 1294 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6827 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1777 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 317} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 343} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1072 Unresolved non-hydrogen angles: 1365 Unresolved non-hydrogen dihedrals: 888 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 26, 'PHE:plan': 20, 'GLU:plan': 15, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 562 Chain: "B" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 5050 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 446} Link IDs: {'PTRANS': 46, 'TRANS': 783} Chain breaks: 26 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1646 Unresolved non-hydrogen angles: 2113 Unresolved non-hydrogen dihedrals: 1370 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 24, 'TYR:plan': 15, 'ASN:plan1': 6, 'TRP:plan': 7, 'HIS:plan': 17, 'PHE:plan': 17, 'GLU:plan': 39, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 878 Time building chain proxies: 6.59, per 1000 atoms: 0.97 Number of scatterers: 6827 At special positions: 0 Unit cell: (65.45, 96.05, 210.8, 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 15 16.00 O 1340 8.00 N 1294 7.00 C 4178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 32 sheets defined 11.8% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 91 through 94 No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'B' and resid 292 through 304 removed outlier: 4.642A pdb=" N GLN B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 Processing helix chain 'B' and resid 600 through 609 removed outlier: 4.376A pdb=" N LEU B 606 " --> pdb=" O ARG B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 828 through 841 removed outlier: 4.076A pdb=" N ILE B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR B 834 " --> pdb=" O TYR B 830 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN B 839 " --> pdb=" O ASN B 835 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1093 removed outlier: 3.887A pdb=" N LEU B1093 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1224 through 1237 Processing helix chain 'B' and resid 1591 through 1591 No H-bonds generated for 'chain 'B' and resid 1591 through 1591' Processing helix chain 'B' and resid 1595 through 1607 Processing helix chain 'B' and resid 1691 through 1699 Processing helix chain 'B' and resid 1722 through 1729 Processing sheet with id=1, first strand: chain 'A' and resid 9 through 14 No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 20 through 25 No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'A' and resid 28 through 33 No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'A' and resid 38 through 43 No H-bonds generated for sheet with id=4 Processing sheet with id=5, first strand: chain 'A' and resid 51 through 56 No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'A' and resid 62 through 67 No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'A' and resid 78 through 83 No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'A' and resid 95 through 100 No H-bonds generated for sheet with id=8 Processing sheet with id=9, first strand: chain 'A' and resid 105 through 111 No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'A' and resid 114 through 119 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'A' and resid 122 through 127 No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'A' and resid 134 through 139 No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'A' and resid 148 through 150 No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'A' and resid 158 through 162 No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'A' and resid 168 through 173 No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'A' and resid 186 through 189 No H-bonds generated for sheet with id=16 Processing sheet with id=17, first strand: chain 'A' and resid 195 through 200 No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'A' and resid 206 through 211 No H-bonds generated for sheet with id=18 Processing sheet with id=19, first strand: chain 'A' and resid 216 through 221 No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'A' and resid 227 through 232 No H-bonds generated for sheet with id=20 Processing sheet with id=21, first strand: chain 'A' and resid 240 through 245 No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'A' and resid 251 through 256 No H-bonds generated for sheet with id=22 Processing sheet with id=23, first strand: chain 'A' and resid 260 through 265 No H-bonds generated for sheet with id=23 Processing sheet with id=24, first strand: chain 'A' and resid 298 through 301 No H-bonds generated for sheet with id=24 Processing sheet with id=25, first strand: chain 'A' and resid 308 through 312 No H-bonds generated for sheet with id=25 Processing sheet with id=26, first strand: chain 'A' and resid 320 through 327 No H-bonds generated for sheet with id=26 Processing sheet with id=27, first strand: chain 'A' and resid 331 through 338 No H-bonds generated for sheet with id=27 Processing sheet with id=28, first strand: chain 'A' and resid 343 through 350 No H-bonds generated for sheet with id=28 Processing sheet with id=A, first strand: chain 'B' and resid 173 through 176 removed outlier: 7.738A pdb=" N ASP B 173 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASP B 202 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 175 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 200 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU B 198 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 229 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR B 200 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 227 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 202 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS B 225 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 223 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 265 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS B 225 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 263 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 227 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 261 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 229 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET B 259 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B 260 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN B 281 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET B 262 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 279 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 264 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLU B 277 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B 426 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 278 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 428 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY B 280 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N THR B 430 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 282 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER B 425 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 501 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 427 " --> pdb=" O TRP B 499 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TRP B 499 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 429 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 497 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU B 431 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 495 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 496 " --> pdb=" O HIS B 516 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS B 516 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 514 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER B 512 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 502 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B 509 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 564 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR B 511 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN B 562 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N MET B 513 " --> pdb=" O HIS B 560 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 558 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 556 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS B 557 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP B 587 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG B 559 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 585 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 561 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B 583 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 563 " --> pdb=" O HIS B 581 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS B 581 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 565 " --> pdb=" O HIS B 579 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS B 579 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLU B 629 " --> pdb=" O CYS B 580 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N SER B 582 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN B 631 " --> pdb=" O SER B 582 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 584 " --> pdb=" O GLN B 631 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 633 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 586 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG B 635 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 588 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER B 637 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N GLN B 630 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 684 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU B 636 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE B 678 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLN B 677 " --> pdb=" O THR B 697 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR B 697 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG B 679 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 695 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 681 " --> pdb=" O HIS B 693 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS B 693 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 696 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 736 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 735 " --> pdb=" O ILE B 816 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR B 739 " --> pdb=" O SER B 812 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER B 812 " --> pdb=" O THR B 739 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 927 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 813 " --> pdb=" O SER B 927 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 929 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 931 " --> pdb=" O VAL B 815 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 926 " --> pdb=" O SER B 971 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 971 " --> pdb=" O PHE B 926 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 969 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 967 " --> pdb=" O VAL B 930 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU B 985 " --> pdb=" O THR B 966 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 968 " --> pdb=" O CYS B 983 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 983 " --> pdb=" O PHE B 968 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B 970 " --> pdb=" O TYR B 981 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 981 " --> pdb=" O VAL B 970 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 980 " --> pdb=" O ILE B1052 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B1052 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 982 " --> pdb=" O VAL B1050 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 984 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA B 986 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B1046 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG B1068 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B1049 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B1066 " --> pdb=" O ALA B1049 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N HIS B1053 " --> pdb=" O GLU B1062 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B1062 " --> pdb=" O HIS B1053 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP B1055 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B1060 " --> pdb=" O ASP B1055 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B1107 " --> pdb=" O LYS B1061 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE B1063 " --> pdb=" O THR B1107 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE B1109 " --> pdb=" O PHE B1063 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N VAL B1065 " --> pdb=" O ILE B1109 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE B1111 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU B1067 " --> pdb=" O ILE B1111 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N HIS B1113 " --> pdb=" O LEU B1067 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU B1069 " --> pdb=" O HIS B1113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N HIS B1115 " --> pdb=" O LEU B1069 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR B1110 " --> pdb=" O ILE B1145 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B1145 " --> pdb=" O THR B1110 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU B1112 " --> pdb=" O SER B1143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1114 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B1141 " --> pdb=" O THR B1114 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B1138 " --> pdb=" O ASP B1159 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP B1159 " --> pdb=" O THR B1138 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B1140 " --> pdb=" O ILE B1157 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B1157 " --> pdb=" O THR B1140 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B1142 " --> pdb=" O ARG B1155 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B1155 " --> pdb=" O SER B1142 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B1144 " --> pdb=" O LEU B1153 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B1153 " --> pdb=" O ASN B1144 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE B1146 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR B1151 " --> pdb=" O ILE B1146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B1156 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B1191 " --> pdb=" O PHE B1156 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B1158 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B1189 " --> pdb=" O LEU B1158 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B1190 " --> pdb=" O SER B1214 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER B1214 " --> pdb=" O GLU B1190 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B1192 " --> pdb=" O ARG B1212 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG B1212 " --> pdb=" O VAL B1192 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS B1194 " --> pdb=" O GLU B1210 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B1210 " --> pdb=" O LYS B1194 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG B1418 " --> pdb=" O PHE B1209 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B1211 " --> pdb=" O ARG B1418 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL B1420 " --> pdb=" O LEU B1211 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS B1213 " --> pdb=" O VAL B1420 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG B1422 " --> pdb=" O CYS B1213 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN B1215 " --> pdb=" O ARG B1422 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR B1417 " --> pdb=" O VAL B1495 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B1495 " --> pdb=" O THR B1417 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL B1419 " --> pdb=" O HIS B1493 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS B1493 " --> pdb=" O VAL B1419 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B1421 " --> pdb=" O PHE B1491 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE B1491 " --> pdb=" O LEU B1421 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B1490 " --> pdb=" O ILE B1522 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B1522 " --> pdb=" O SER B1490 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B1492 " --> pdb=" O VAL B1520 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B1520 " --> pdb=" O GLN B1492 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU B1494 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG B1518 " --> pdb=" O GLU B1494 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B1516 " --> pdb=" O HIS B1564 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS B1564 " --> pdb=" O LEU B1516 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ARG B1518 " --> pdb=" O ALA B1562 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B1562 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N VAL B1520 " --> pdb=" O ILE B1560 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE B1560 " --> pdb=" O VAL B1520 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE B1522 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B1558 " --> pdb=" O ILE B1522 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B1559 " --> pdb=" O SER B1581 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B1581 " --> pdb=" O THR B1559 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS B1561 " --> pdb=" O ARG B1579 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG B1579 " --> pdb=" O LYS B1561 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU B1563 " --> pdb=" O CYS B1577 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N CYS B1577 " --> pdb=" O LEU B1563 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B1666 " --> pdb=" O CYS B1576 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B1578 " --> pdb=" O GLU B1666 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG B1668 " --> pdb=" O LEU B1578 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B1580 " --> pdb=" O ARG B1668 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR B1670 " --> pdb=" O VAL B1580 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU B1582 " --> pdb=" O THR B1670 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE B1667 " --> pdb=" O CYS B1714 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N CYS B1714 " --> pdb=" O PHE B1667 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B1669 " --> pdb=" O LEU B1712 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B1712 " --> pdb=" O PHE B1669 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'B' and resid 536 through 543 removed outlier: 12.200A pdb=" N TYR B 536 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N GLU B 524 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU B 538 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 522 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 540 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU B 520 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N GLN B 519 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N THR B 493 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLU B 521 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N THR B 491 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 523 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ARG B 489 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B 488 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 438 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 436 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY B 492 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL B 434 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N LEU B 285 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR B 435 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LEU B 287 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 437 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU B 289 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU B 439 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 284 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER B 256 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N HIS B 286 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N SER B 254 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU B 288 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ILE B 252 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N THR B 290 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 13.602A pdb=" N LEU B 250 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 250 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N TYR B 236 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE B 252 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 234 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER B 254 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 232 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 194 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 234 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N GLU B 192 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 193 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS B 180 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL B 195 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 178 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 591 through 597 removed outlier: 4.458A pdb=" N ALA B 641 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 593 " --> pdb=" O ALA B 641 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 643 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 595 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 645 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 597 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA B 641 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 673 " --> pdb=" O ALA B 641 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 643 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 671 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 645 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU B 669 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN B 668 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 706 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 672 " --> pdb=" O HIS B 702 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N HIS B 702 " --> pdb=" O GLU B 672 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER B 674 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASP B 700 " --> pdb=" O SER B 674 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 701 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 718 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY B 703 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU B 716 " --> pdb=" O GLY B 703 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR B 705 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N CYS B 715 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 823 " --> pdb=" O CYS B 715 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG B 717 " --> pdb=" O HIS B 821 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N HIS B 821 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER B 719 " --> pdb=" O SER B 819 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER B 819 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 820 " --> pdb=" O LYS B 934 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG B 936 " --> pdb=" O VAL B 820 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE B 822 " --> pdb=" O ARG B 936 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 938 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU B 824 " --> pdb=" O THR B 938 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 962 " --> pdb=" O GLY B 935 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 937 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 960 " --> pdb=" O ILE B 937 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA B 939 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N LEU B 958 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 958 " --> pdb=" O HIS B 993 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS B 993 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LEU B 960 " --> pdb=" O LEU B 991 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N LEU B 991 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET B 962 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA B 989 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N ALA B 989 " --> pdb=" O PRO B1023 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 991 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS B 993 " --> pdb=" O PRO B1019 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR B1020 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N ARG B1075 " --> pdb=" O THR B1020 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B1022 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR B1073 " --> pdb=" O TYR B1022 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N SER B1120 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N HIS B1076 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 13.226A pdb=" N ASP B1122 " --> pdb=" O HIS B1076 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N CYS B1119 " --> pdb=" O ALA B1136 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA B1136 " --> pdb=" O CYS B1119 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B1123 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL B1132 " --> pdb=" O TYR B1123 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG B1131 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER B1166 " --> pdb=" O ARG B1131 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B1135 " --> pdb=" O ALA B1162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B1162 " --> pdb=" O THR B1135 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B1163 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B1184 " --> pdb=" O LEU B1163 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B1165 " --> pdb=" O CYS B1182 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N CYS B1182 " --> pdb=" O LEU B1165 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B1183 " --> pdb=" O HIS B1221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B1221 " --> pdb=" O VAL B1183 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL B1424 " --> pdb=" O VAL B1218 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1220 " --> pdb=" O VAL B1424 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B1426 " --> pdb=" O VAL B1220 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N SER B1222 " --> pdb=" O LEU B1426 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TRP B1428 " --> pdb=" O SER B1222 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B1486 " --> pdb=" O VAL B1424 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B1426 " --> pdb=" O ILE B1484 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE B1484 " --> pdb=" O LEU B1426 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP B1428 " --> pdb=" O MET B1482 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLU B1483 " --> pdb=" O ARG B1529 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B1529 " --> pdb=" O GLU B1483 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B1527 " --> pdb=" O GLN B1485 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 1539 through 1542 removed outlier: 5.264A pdb=" N PHE B1540 " --> pdb=" O ASN B1588 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B1588 " --> pdb=" O PHE B1540 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR B1542 " --> pdb=" O ARG B1586 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N ARG B1586 " --> pdb=" O TYR B1542 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU B1585 " --> pdb=" O PRO B1674 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP B1676 " --> pdb=" O LEU B1585 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B1587 " --> pdb=" O TRP B1676 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B1589 " --> pdb=" O ASP B1678 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B1673 " --> pdb=" O LEU B1709 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1709 " --> pdb=" O VAL B1673 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B1675 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B1707 " --> pdb=" O ILE B1675 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER B1705 " --> pdb=" O LEU B1677 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 354 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: 2.93 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2119 1.33 - 1.45: 742 1.45 - 1.57: 3975 1.57 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 6853 Sorted by residual: bond pdb=" CA ARG B 646 " pdb=" C ARG B 646 " ideal model delta sigma weight residual 1.522 1.495 0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" N LEU B 673 " pdb=" CA LEU B 673 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.51e+00 bond pdb=" CA VAL A 283 " pdb=" CB VAL A 283 " ideal model delta sigma weight residual 1.527 1.554 -0.027 1.31e-02 5.83e+03 4.39e+00 bond pdb=" N ARG B 670 " pdb=" CA ARG B 670 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.19e-02 7.06e+03 4.32e+00 bond pdb=" N LEU B 671 " pdb=" CA LEU B 671 " ideal model delta sigma weight residual 1.464 1.437 0.027 1.30e-02 5.92e+03 4.18e+00 ... (remaining 6848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 9050 2.49 - 4.98: 348 4.98 - 7.47: 27 7.47 - 9.97: 5 9.97 - 12.46: 4 Bond angle restraints: 9434 Sorted by residual: angle pdb=" N ALA B 599 " pdb=" CA ALA B 599 " pdb=" C ALA B 599 " ideal model delta sigma weight residual 108.76 121.22 -12.46 1.58e+00 4.01e-01 6.22e+01 angle pdb=" C GLN B 677 " pdb=" CA GLN B 677 " pdb=" CB GLN B 677 " ideal model delta sigma weight residual 116.34 105.75 10.59 1.40e+00 5.10e-01 5.72e+01 angle pdb=" N ARG B 670 " pdb=" CA ARG B 670 " pdb=" C ARG B 670 " ideal model delta sigma weight residual 108.34 118.41 -10.07 1.64e+00 3.72e-01 3.77e+01 angle pdb=" N LEU B 671 " pdb=" CA LEU B 671 " pdb=" C LEU B 671 " ideal model delta sigma weight residual 109.62 101.58 8.04 1.50e+00 4.44e-01 2.88e+01 angle pdb=" N GLN B 677 " pdb=" CA GLN B 677 " pdb=" C GLN B 677 " ideal model delta sigma weight residual 108.00 115.74 -7.74 1.48e+00 4.57e-01 2.74e+01 ... (remaining 9429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 3808 17.33 - 34.67: 182 34.67 - 52.00: 45 52.00 - 69.34: 4 69.34 - 86.67: 6 Dihedral angle restraints: 4045 sinusoidal: 610 harmonic: 3435 Sorted by residual: dihedral pdb=" CA ASP A 359 " pdb=" C ASP A 359 " pdb=" N PHE A 360 " pdb=" CA PHE A 360 " ideal model delta harmonic sigma weight residual 180.00 138.87 41.13 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N SER A 183 " pdb=" CA SER A 183 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU B1170 " pdb=" C GLU B1170 " pdb=" N VAL B1171 " pdb=" CA VAL B1171 " ideal model delta harmonic sigma weight residual 180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 913 0.057 - 0.114: 262 0.114 - 0.170: 74 0.170 - 0.227: 11 0.227 - 0.284: 4 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CA MET A 286 " pdb=" N MET A 286 " pdb=" C MET A 286 " pdb=" CB MET A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR A 331 " pdb=" N THR A 331 " pdb=" C THR A 331 " pdb=" CB THR A 331 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PHE A 186 " pdb=" N PHE A 186 " pdb=" C PHE A 186 " pdb=" CB PHE A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1261 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 114 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C LYS A 114 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS A 114 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 115 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 1 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C MET A 1 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 1 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 2 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 39 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C GLU A 39 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU A 39 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 40 " 0.013 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 1 2.24 - 2.90: 2978 2.90 - 3.57: 8923 3.57 - 4.23: 12924 4.23 - 4.90: 21694 Nonbonded interactions: 46520 Sorted by model distance: nonbonded pdb=" CB GLU A 87 " pdb=" CB ARG B1711 " model vdw 1.571 3.840 nonbonded pdb=" O LEU B1604 " pdb=" N ILE B1608 " model vdw 2.288 3.120 nonbonded pdb=" O SER B 819 " pdb=" OG SER B 819 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR B 834 " pdb=" N ASP B1097 " model vdw 2.300 3.120 nonbonded pdb=" OD1 ASN B1215 " pdb=" N ASN B1216 " model vdw 2.346 3.120 ... (remaining 46515 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3258 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 : 0.005 0.033 6853 Z= 0.373 Angle : 1.098 12.457 9434 Z= 0.697 Chirality : 0.059 0.284 1264 Planarity : 0.005 0.039 1284 Dihedral : 13.377 86.670 1779 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.35 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 26.97 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.22), residues: 1134 helix: -0.59 (0.50), residues: 112 sheet: -0.86 (0.35), residues: 186 loop : -3.33 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.003 0.001 HIS B 560 PHE 0.037 0.001 PHE B1092 TYR 0.012 0.001 TYR B 834 ARG 0.006 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.758 Fit side-chains REVERT: B 1210 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6059 (tm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1667 time to fit residues: 9.7681 Evaluate side-chains 29 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5415 r_free = 0.5415 target = 0.240147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.5071 r_free = 0.5071 target = 0.199352 restraints weight = 9477.537| |-----------------------------------------------------------------------------| r_work (start): 0.5045 rms_B_bonded: 2.34 r_work: 0.4892 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6853 Z= 0.212 Angle : 0.683 8.596 9434 Z= 0.365 Chirality : 0.046 0.205 1264 Planarity : 0.004 0.042 1284 Dihedral : 5.941 24.609 1185 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.25 % Allowed : 22.70 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.23), residues: 1134 helix: -0.54 (0.50), residues: 108 sheet: -0.63 (0.36), residues: 195 loop : -3.06 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.003 0.001 HIS B1115 PHE 0.026 0.002 PHE B 634 TYR 0.013 0.002 TYR B1022 ARG 0.004 0.001 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.690 Fit side-chains REVERT: B 1193 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6399 (mp) outliers start: 19 outliers final: 11 residues processed: 46 average time/residue: 0.1207 time to fit residues: 9.5037 Evaluate side-chains 39 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Chi-restraints excluded: chain B residue 1612 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5334 r_free = 0.5334 target = 0.228255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.197928 restraints weight = 10032.447| |-----------------------------------------------------------------------------| r_work (start): 0.5086 rms_B_bonded: 1.95 r_work: 0.4897 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6853 Z= 0.297 Angle : 0.759 9.048 9434 Z= 0.412 Chirality : 0.049 0.248 1264 Planarity : 0.005 0.049 1284 Dihedral : 6.805 28.508 1185 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.64 % Favored : 85.36 % Rotamer: Outliers : 9.21 % Allowed : 22.37 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.23), residues: 1134 helix: -0.79 (0.49), residues: 102 sheet: -1.12 (0.36), residues: 193 loop : -3.18 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.006 0.002 HIS B1113 PHE 0.046 0.003 PHE B 634 TYR 0.026 0.003 TYR B1022 ARG 0.006 0.001 ARG B 602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 30 time to evaluate : 0.713 Fit side-chains REVERT: B 228 GLN cc_start: 0.5163 (OUTLIER) cc_final: 0.4768 (tt0) REVERT: B 1156 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6766 (m-80) outliers start: 28 outliers final: 18 residues processed: 55 average time/residue: 0.1088 time to fit residues: 10.2525 Evaluate side-chains 49 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1599 ASP Chi-restraints excluded: chain B residue 1609 ASN Chi-restraints excluded: chain B residue 1612 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 50 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5417 r_free = 0.5417 target = 0.238562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.5181 r_free = 0.5181 target = 0.205274 restraints weight = 9638.008| |-----------------------------------------------------------------------------| r_work (start): 0.5162 rms_B_bonded: 2.02 r_work: 0.4962 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5433 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6853 Z= 0.165 Angle : 0.620 8.489 9434 Z= 0.334 Chirality : 0.045 0.173 1264 Planarity : 0.003 0.040 1284 Dihedral : 5.862 24.073 1185 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 6.25 % Allowed : 26.32 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.23), residues: 1134 helix: -0.48 (0.50), residues: 102 sheet: -0.69 (0.37), residues: 180 loop : -3.12 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.005 0.001 HIS B1115 PHE 0.026 0.002 PHE B 634 TYR 0.012 0.001 TYR B 834 ARG 0.003 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.738 Fit side-chains REVERT: B 228 GLN cc_start: 0.5234 (OUTLIER) cc_final: 0.4824 (tt0) REVERT: B 1062 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5390 (tm-30) REVERT: B 1193 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6408 (mp) outliers start: 19 outliers final: 13 residues processed: 50 average time/residue: 0.1416 time to fit residues: 11.2793 Evaluate side-chains 46 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1609 ASN Chi-restraints excluded: chain B residue 1612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 118 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 36 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.230498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.195627 restraints weight = 9764.464| |-----------------------------------------------------------------------------| r_work (start): 0.5044 rms_B_bonded: 1.98 r_work: 0.4867 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 6853 Z= 0.424 Angle : 0.889 10.419 9434 Z= 0.483 Chirality : 0.052 0.331 1264 Planarity : 0.006 0.082 1284 Dihedral : 7.598 29.266 1185 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.17 % Favored : 81.75 % Rotamer: Outliers : 9.54 % Allowed : 25.00 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.22), residues: 1134 helix: -1.37 (0.46), residues: 102 sheet: -1.47 (0.39), residues: 169 loop : -3.47 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.014 0.003 HIS B1115 PHE 0.065 0.004 PHE B 634 TYR 0.027 0.003 TYR B 834 ARG 0.007 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 29 time to evaluate : 0.763 Fit side-chains REVERT: B 228 GLN cc_start: 0.5330 (OUTLIER) cc_final: 0.4925 (tt0) REVERT: B 1156 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7057 (m-10) REVERT: B 1193 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6611 (mp) outliers start: 29 outliers final: 15 residues processed: 56 average time/residue: 0.0993 time to fit residues: 9.7978 Evaluate side-chains 47 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1110 THR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.229957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.195437 restraints weight = 9762.388| |-----------------------------------------------------------------------------| r_work (start): 0.5041 rms_B_bonded: 1.97 r_work: 0.4865 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 6853 Z= 0.379 Angle : 0.859 10.061 9434 Z= 0.464 Chirality : 0.051 0.276 1264 Planarity : 0.006 0.085 1284 Dihedral : 7.613 29.926 1185 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.58 % Favored : 83.42 % Rotamer: Outliers : 9.54 % Allowed : 25.00 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.22), residues: 1134 helix: -1.87 (0.43), residues: 110 sheet: -2.03 (0.41), residues: 144 loop : -3.56 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.007 0.002 HIS B1113 PHE 0.055 0.004 PHE B 634 TYR 0.020 0.002 TYR B 834 ARG 0.007 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 29 time to evaluate : 0.721 Fit side-chains REVERT: B 228 GLN cc_start: 0.5317 (OUTLIER) cc_final: 0.4910 (tt0) REVERT: B 1156 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6968 (m-10) outliers start: 29 outliers final: 20 residues processed: 56 average time/residue: 0.1052 time to fit residues: 10.1022 Evaluate side-chains 50 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 28 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1110 THR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5281 r_free = 0.5281 target = 0.227205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.5030 r_free = 0.5030 target = 0.193829 restraints weight = 9961.256| |-----------------------------------------------------------------------------| r_work (start): 0.4993 rms_B_bonded: 1.92 r_work: 0.4820 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4717 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6853 Z= 0.340 Angle : 0.807 9.363 9434 Z= 0.438 Chirality : 0.049 0.258 1264 Planarity : 0.005 0.083 1284 Dihedral : 7.355 28.971 1185 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 9.54 % Allowed : 26.32 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.21), residues: 1134 helix: -1.74 (0.44), residues: 110 sheet: -2.02 (0.46), residues: 116 loop : -3.64 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.007 0.002 HIS B1115 PHE 0.047 0.003 PHE B 634 TYR 0.019 0.002 TYR B 834 ARG 0.010 0.001 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 30 time to evaluate : 0.764 Fit side-chains REVERT: B 228 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.4973 (tt0) REVERT: B 1156 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: B 1193 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6495 (mp) outliers start: 29 outliers final: 20 residues processed: 56 average time/residue: 0.1029 time to fit residues: 9.8154 Evaluate side-chains 52 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain B residue 1052 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1110 THR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain B residue 1168 LYS Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 30.0000 chunk 41 optimal weight: 0.0000 chunk 20 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.0470 chunk 23 optimal weight: 0.4980 chunk 89 optimal weight: 0.0970 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.232065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.5043 r_free = 0.5043 target = 0.195307 restraints weight = 9914.082| |-----------------------------------------------------------------------------| r_work (start): 0.5004 rms_B_bonded: 2.84 r_work: 0.4851 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6853 Z= 0.146 Angle : 0.602 8.251 9434 Z= 0.325 Chirality : 0.045 0.166 1264 Planarity : 0.003 0.058 1284 Dihedral : 5.783 27.325 1185 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 5.59 % Allowed : 30.26 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.22), residues: 1134 helix: -1.05 (0.48), residues: 110 sheet: -2.13 (0.42), residues: 140 loop : -3.36 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.006 0.001 HIS B 560 PHE 0.012 0.001 PHE B1092 TYR 0.009 0.001 TYR B 834 ARG 0.004 0.001 ARG B1075 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.760 Fit side-chains REVERT: B 228 GLN cc_start: 0.4957 (OUTLIER) cc_final: 0.4529 (tt0) REVERT: B 1062 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5535 (tm-30) outliers start: 17 outliers final: 13 residues processed: 49 average time/residue: 0.1272 time to fit residues: 10.1257 Evaluate side-chains 45 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 HIS Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1168 LYS Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN B1556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.222071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.4867 r_free = 0.4867 target = 0.182689 restraints weight = 10171.347| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 2.62 r_work: 0.4692 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.139 6853 Z= 0.567 Angle : 1.025 12.917 9434 Z= 0.557 Chirality : 0.056 0.484 1264 Planarity : 0.008 0.152 1284 Dihedral : 8.334 30.749 1185 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.62 % Allowed : 21.08 % Favored : 78.31 % Rotamer: Outliers : 8.22 % Allowed : 30.26 % Favored : 61.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.21), residues: 1134 helix: -2.07 (0.43), residues: 109 sheet: -2.55 (0.44), residues: 114 loop : -3.81 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.014 0.003 HIS B1115 PHE 0.035 0.005 PHE B 926 TYR 0.019 0.003 TYR B 834 ARG 0.010 0.002 ARG B1586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 27 time to evaluate : 0.715 Fit side-chains REVERT: B 228 GLN cc_start: 0.5428 (OUTLIER) cc_final: 0.4975 (tt0) outliers start: 25 outliers final: 16 residues processed: 51 average time/residue: 0.1064 time to fit residues: 9.4068 Evaluate side-chains 44 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 27 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1168 LYS Chi-restraints excluded: chain B residue 1226 SER Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 101 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.231290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.198012 restraints weight = 9866.292| |-----------------------------------------------------------------------------| r_work (start): 0.5063 rms_B_bonded: 1.94 r_work: 0.4892 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4794 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6853 Z= 0.179 Angle : 0.668 10.407 9434 Z= 0.363 Chirality : 0.046 0.175 1264 Planarity : 0.004 0.061 1284 Dihedral : 6.337 28.294 1185 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 5.59 % Allowed : 32.24 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.22), residues: 1134 helix: -1.31 (0.48), residues: 109 sheet: -2.67 (0.40), residues: 142 loop : -3.51 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.005 0.001 HIS B 560 PHE 0.014 0.001 PHE B1092 TYR 0.012 0.001 TYR B 834 ARG 0.003 0.001 ARG B1075 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.762 Fit side-chains REVERT: B 228 GLN cc_start: 0.5231 (OUTLIER) cc_final: 0.4838 (tt0) REVERT: B 1059 ASN cc_start: 0.4335 (OUTLIER) cc_final: 0.4134 (t0) REVERT: B 1062 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5707 (tm-30) outliers start: 17 outliers final: 14 residues processed: 45 average time/residue: 0.1085 time to fit residues: 8.5934 Evaluate side-chains 46 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 966 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain B residue 1103 TYR Chi-restraints excluded: chain B residue 1168 LYS Chi-restraints excluded: chain B residue 1421 LEU Chi-restraints excluded: chain B residue 1609 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.6980 chunk 9 optimal weight: 0.0070 chunk 6 optimal weight: 5.9990 chunk 89 optimal weight: 0.0040 chunk 36 optimal weight: 0.0470 chunk 108 optimal weight: 4.9990 chunk 29 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.229147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.197676 restraints weight = 9913.109| |-----------------------------------------------------------------------------| r_work (start): 0.5091 rms_B_bonded: 2.00 r_work: 0.4877 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 6853 Z= 0.241 Angle : 1.039 59.123 9434 Z= 0.621 Chirality : 0.047 0.398 1264 Planarity : 0.004 0.059 1284 Dihedral : 6.350 28.125 1185 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.23 % Favored : 86.68 % Rotamer: Outliers : 5.59 % Allowed : 32.57 % Favored : 61.84 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.22), residues: 1134 helix: -1.25 (0.48), residues: 109 sheet: -2.64 (0.40), residues: 142 loop : -3.50 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 82 HIS 0.005 0.001 HIS B1115 PHE 0.014 0.001 PHE B1092 TYR 0.009 0.001 TYR B 200 ARG 0.003 0.000 ARG B1075 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.54 seconds wall clock time: 78 minutes 56.73 seconds (4736.73 seconds total)