Starting phenix.real_space_refine on Mon May 4 22:46:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh7_64157/05_2026/9uh7_64157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh7_64157/05_2026/9uh7_64157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uh7_64157/05_2026/9uh7_64157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh7_64157/05_2026/9uh7_64157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uh7_64157/05_2026/9uh7_64157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh7_64157/05_2026/9uh7_64157.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 204 5.49 5 S 111 5.16 5 C 14684 2.51 5 N 4264 2.21 5 O 5004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24267 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 4320 Classifications: {'RNA': 204} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 80, 'rna3p_pyr': 93} Link IDs: {'rna2p': 31, 'rna3p': 172} Chain breaks: 1 Chain: "B" Number of atoms: 5689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5689 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 47, 'TRANS': 670} Chain breaks: 6 Chain: "D" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1502 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "E" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1224 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain breaks: 1 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1829 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "J" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1916 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain: "K" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 260 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "L" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2939 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 341} Chain: "M" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1828 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Time building chain proxies: 5.24, per 1000 atoms: 0.22 Number of scatterers: 24267 At special positions: 0 Unit cell: (148.5, 165, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 204 15.00 O 5004 8.00 N 4264 7.00 C 14684 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 15 sheets defined 44.0% alpha, 18.4% beta 11 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.591A pdb=" N ARG B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.214A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.616A pdb=" N LYS B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.721A pdb=" N ILE B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 4.120A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.626A pdb=" N GLU B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 551 through 554 removed outlier: 4.175A pdb=" N TRP B 554 " --> pdb=" O SER B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.713A pdb=" N MET B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 638 removed outlier: 3.772A pdb=" N TRP B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 632 " --> pdb=" O MET B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix removed outlier: 3.506A pdb=" N GLY B 638 " --> pdb=" O PHE B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 655 Processing helix chain 'B' and resid 666 through 685 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.545A pdb=" N LEU B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 removed outlier: 3.530A pdb=" N THR B 712 " --> pdb=" O TRP B 708 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 820 removed outlier: 3.752A pdb=" N GLN B 814 " --> pdb=" O LYS B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.511A pdb=" N PHE B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 884 " --> pdb=" O LYS B 880 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 919 removed outlier: 3.889A pdb=" N LEU B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 910 " --> pdb=" O SER B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 959 removed outlier: 4.734A pdb=" N CYS B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 removed outlier: 3.856A pdb=" N ASP B 992 " --> pdb=" O THR B 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 17 removed outlier: 3.966A pdb=" N SER D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 43 through 53 removed outlier: 4.074A pdb=" N ARG D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 84 removed outlier: 3.681A pdb=" N LEU D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 114 removed outlier: 3.567A pdb=" N CYS D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.654A pdb=" N LEU E 22 " --> pdb=" O PRO E 18 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 106 through 126 removed outlier: 3.705A pdb=" N CYS E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 removed outlier: 3.513A pdb=" N ALA E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLN E 139 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 removed outlier: 3.830A pdb=" N LEU E 147 " --> pdb=" O ARG E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'F' and resid 45 through 59 removed outlier: 3.778A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'G' and resid 44 through 58 Processing helix chain 'G' and resid 76 through 92 Processing helix chain 'H' and resid 36 through 53 removed outlier: 4.262A pdb=" N LEU H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'I' and resid 14 through 29 removed outlier: 3.625A pdb=" N LEU I 18 " --> pdb=" O ASP I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.135A pdb=" N LEU I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 100 Processing helix chain 'I' and resid 109 through 117 removed outlier: 3.681A pdb=" N CYS I 117 " --> pdb=" O PHE I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 156 through 162 removed outlier: 3.544A pdb=" N ASP I 162 " --> pdb=" O PRO I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 180 removed outlier: 3.734A pdb=" N ARG I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR I 168 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 197 Processing helix chain 'I' and resid 199 through 211 removed outlier: 3.529A pdb=" N ASN I 205 " --> pdb=" O TYR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 222 through 238 removed outlier: 3.682A pdb=" N ARG I 226 " --> pdb=" O SER I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.665A pdb=" N LEU J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 Processing helix chain 'J' and resid 87 through 92 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.563A pdb=" N CYS J 117 " --> pdb=" O PHE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 156 through 162 removed outlier: 3.753A pdb=" N ILE J 160 " --> pdb=" O TYR J 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 161 " --> pdb=" O SER J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 180 removed outlier: 3.777A pdb=" N ARG J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 211 removed outlier: 3.629A pdb=" N ASN J 205 " --> pdb=" O TYR J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 222 through 238 removed outlier: 3.878A pdb=" N ARG J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA J 238 " --> pdb=" O THR J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.587A pdb=" N LEU K 7 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA K 10 " --> pdb=" O TYR K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 removed outlier: 4.342A pdb=" N ALA K 22 " --> pdb=" O CYS K 18 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS K 33 " --> pdb=" O TYR K 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 9 Processing helix chain 'L' and resid 28 through 36 removed outlier: 3.625A pdb=" N HIS L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 62 Processing helix chain 'L' and resid 75 through 78 removed outlier: 3.543A pdb=" N ILE L 78 " --> pdb=" O HIS L 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 75 through 78' Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 120 through 128 removed outlier: 3.624A pdb=" N GLY L 128 " --> pdb=" O TYR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.667A pdb=" N LEU L 155 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 192 through 197 Processing helix chain 'L' and resid 236 through 249 removed outlier: 3.649A pdb=" N LEU L 240 " --> pdb=" O ARG L 236 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP L 242 " --> pdb=" O LEU L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 Processing helix chain 'M' and resid 10 through 14 Processing helix chain 'M' and resid 32 through 54 Processing helix chain 'M' and resid 55 through 72 removed outlier: 3.573A pdb=" N ASP M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 97 Processing helix chain 'M' and resid 99 through 113 removed outlier: 3.895A pdb=" N LEU M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE M 111 " --> pdb=" O LEU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 165 removed outlier: 3.636A pdb=" N GLY M 165 " --> pdb=" O VAL M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 196 removed outlier: 3.798A pdb=" N LEU M 196 " --> pdb=" O LYS M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 212 removed outlier: 3.794A pdb=" N LEU M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 231 Processing helix chain 'M' and resid 231 through 239 removed outlier: 3.781A pdb=" N PHE M 235 " --> pdb=" O GLY M 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.370A pdb=" N HIS B 213 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 509 removed outlier: 5.292A pdb=" N THR B 503 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN B 601 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.852A pdb=" N GLY B 290 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR B 309 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 292 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 294 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 804 through 805 removed outlier: 7.028A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 875 " --> pdb=" O LEU B 964 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 965 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER B 986 " --> pdb=" O GLY B 965 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL B 967 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 984 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 971 " --> pdb=" O GLU B 980 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 980 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 978 " --> pdb=" O SER B 973 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 174 through 178 removed outlier: 7.298A pdb=" N ILE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU D 160 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS D 166 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE D 139 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU D 187 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 143 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL D 183 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.880A pdb=" N HIS E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU E 12 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR E 100 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 14 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N PHE E 98 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 36 through 39 removed outlier: 5.937A pdb=" N VAL F 36 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N SER F 68 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N MET F 38 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS F 70 " --> pdb=" O MET F 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 20 through 24 removed outlier: 6.754A pdb=" N ILE G 37 " --> pdb=" O HIS G 72 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N LEU G 74 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 14 removed outlier: 3.525A pdb=" N VAL H 11 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU L 15 " --> pdb=" O TYR H 13 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR L 40 " --> pdb=" O GLY L 283 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 61 through 67 removed outlier: 8.135A pdb=" N LEU H 61 " --> pdb=" O CYS H 78 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS H 78 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE H 63 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG H 76 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR H 65 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE H 74 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER H 72 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR H 21 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL H 107 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS H 23 " --> pdb=" O ILE H 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 5 through 10 removed outlier: 4.719A pdb=" N ALA I 5 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA I 34 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU I 7 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN I 36 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU I 9 " --> pdb=" O ASN I 36 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE I 38 " --> pdb=" O LEU I 9 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N VAL I 102 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR I 75 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ALA I 104 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU I 77 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE I 106 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE I 79 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL I 103 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N CYS I 126 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL I 105 " --> pdb=" O CYS I 126 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE I 152 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N SER I 188 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU I 154 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 5 through 6 removed outlier: 7.233A pdb=" N VAL J 39 " --> pdb=" O ILE J 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 5 through 6 removed outlier: 6.703A pdb=" N VAL J 103 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N CYS J 126 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL J 105 " --> pdb=" O CYS J 126 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL J 125 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL J 155 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE J 152 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER J 188 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU J 154 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 132 through 133 removed outlier: 6.757A pdb=" N VAL L 107 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE L 179 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS L 70 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU L 181 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N PHE L 68 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N TRP L 183 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N TYR L 66 " --> pdb=" O TRP L 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 25 through 29 901 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7034 1.34 - 1.46: 5468 1.46 - 1.58: 12131 1.58 - 1.70: 407 1.70 - 1.82: 148 Bond restraints: 25188 Sorted by residual: bond pdb=" N PRO B 301 " pdb=" CD PRO B 301 " ideal model delta sigma weight residual 1.473 1.609 -0.136 1.40e-02 5.10e+03 9.41e+01 bond pdb=" CG LEU M 183 " pdb=" CD2 LEU M 183 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.11e+00 bond pdb=" C VAL B 659 " pdb=" N PRO B 660 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.08e-02 8.57e+03 2.38e+00 bond pdb=" CB GLN M 56 " pdb=" CG GLN M 56 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB GLU E 149 " pdb=" CG GLU E 149 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.27e+00 ... (remaining 25183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.56: 35017 6.56 - 13.12: 37 13.12 - 19.68: 6 19.68 - 26.24: 2 26.24 - 32.80: 2 Bond angle restraints: 35064 Sorted by residual: angle pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" C ALA B 999 " ideal model delta sigma weight residual 112.89 145.69 -32.80 1.24e+00 6.50e-01 7.00e+02 angle pdb=" N PRO B 998 " pdb=" CA PRO B 998 " pdb=" C PRO B 998 " ideal model delta sigma weight residual 110.40 83.17 27.23 1.61e+00 3.86e-01 2.86e+02 angle pdb=" C LYS B 299 " pdb=" CA LYS B 299 " pdb=" CB LYS B 299 " ideal model delta sigma weight residual 110.62 88.70 21.92 1.51e+00 4.39e-01 2.11e+02 angle pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta sigma weight residual 110.40 87.80 22.60 1.63e+00 3.76e-01 1.92e+02 angle pdb=" N ALA B1000 " pdb=" CA ALA B1000 " pdb=" C ALA B1000 " ideal model delta sigma weight residual 113.55 99.21 14.34 1.26e+00 6.30e-01 1.29e+02 ... (remaining 35059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 14664 35.61 - 71.22: 872 71.22 - 106.82: 96 106.82 - 142.43: 0 142.43 - 178.04: 2 Dihedral angle restraints: 15634 sinusoidal: 8297 harmonic: 7337 Sorted by residual: dihedral pdb=" N ALA B 999 " pdb=" C ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta harmonic sigma weight residual 122.90 96.76 26.14 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" C ALA B 999 " pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta harmonic sigma weight residual -122.60 -99.66 -22.94 0 2.50e+00 1.60e-01 8.42e+01 dihedral pdb=" O4' C A 243 " pdb=" C1' C A 243 " pdb=" N1 C A 243 " pdb=" C2 C A 243 " ideal model delta sinusoidal sigma weight residual 232.00 53.96 178.04 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 4109 0.120 - 0.239: 46 0.239 - 0.359: 3 0.359 - 0.478: 0 0.478 - 0.598: 2 Chirality restraints: 4160 Sorted by residual: chirality pdb=" CA ALA B 999 " pdb=" N ALA B 999 " pdb=" C ALA B 999 " pdb=" CB ALA B 999 " both_signs ideal model delta sigma weight residual False 2.48 1.89 0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CA PRO B 998 " pdb=" N PRO B 998 " pdb=" C PRO B 998 " pdb=" CB PRO B 998 " both_signs ideal model delta sigma weight residual False 2.72 3.25 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA TYR B 300 " pdb=" N TYR B 300 " pdb=" C TYR B 300 " pdb=" CB TYR B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4157 not shown) Planarity restraints: 3692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 76 " 0.369 9.50e-02 1.11e+02 1.65e-01 1.68e+01 pdb=" NE ARG H 76 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 76 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG H 76 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 76 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 171 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" CD GLU D 171 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU D 171 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU D 171 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP J 8 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP J 8 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP J 8 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU J 9 " -0.013 2.00e-02 2.50e+03 ... (remaining 3689 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 33 2.59 - 3.16: 18628 3.16 - 3.74: 38628 3.74 - 4.32: 50600 4.32 - 4.90: 80348 Nonbonded interactions: 188237 Sorted by model distance: nonbonded pdb=" N PRO B 998 " pdb=" O PRO B 998 " model vdw 2.008 2.496 nonbonded pdb=" C GLN B 997 " pdb=" O PRO B 998 " model vdw 2.244 3.270 nonbonded pdb=" O LEU D 180 " pdb=" OD1 ASN D 181 " model vdw 2.247 3.040 nonbonded pdb=" O LYS B 299 " pdb=" CB LYS B 299 " model vdw 2.398 2.752 nonbonded pdb=" O ASP J 8 " pdb=" OD1 ASP J 8 " model vdw 2.419 3.040 ... (remaining 188232 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 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 238) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.580 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.003 0.136 25188 Z= 0.139 Angle : 0.756 32.800 35064 Z= 0.404 Chirality : 0.041 0.598 4160 Planarity : 0.005 0.165 3692 Dihedral : 19.700 178.038 10872 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.36 % Allowed : 34.77 % Favored : 64.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2481 helix: 1.28 (0.17), residues: 947 sheet: 0.42 (0.23), residues: 498 loop : -1.55 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 210 TYR 0.025 0.001 TYR E 86 PHE 0.026 0.001 PHE G 45 TRP 0.018 0.001 TRP M 184 HIS 0.014 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00283 (25188) covalent geometry : angle 0.75574 (35064) hydrogen bonds : bond 0.15879 ( 921) hydrogen bonds : angle 5.55461 ( 2637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 231 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 MET cc_start: 0.9274 (mmp) cc_final: 0.9055 (mmt) REVERT: B 849 LEU cc_start: 0.9408 (mm) cc_final: 0.8997 (mm) REVERT: E 118 ASN cc_start: 0.9185 (m-40) cc_final: 0.8820 (m-40) REVERT: F 56 SER cc_start: 0.8756 (m) cc_final: 0.8534 (p) REVERT: F 99 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: G 44 ASP cc_start: 0.7748 (t0) cc_final: 0.7546 (t0) REVERT: G 112 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8660 (mt-10) REVERT: H 29 GLN cc_start: 0.8398 (pp30) cc_final: 0.7998 (pp30) REVERT: I 58 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8358 (t80) REVERT: J 184 ASN cc_start: 0.8987 (m110) cc_final: 0.8776 (m-40) outliers start: 8 outliers final: 5 residues processed: 236 average time/residue: 0.6429 time to fit residues: 174.6784 Evaluate side-chains 201 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain M residue 234 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN D 181 ASN E 111 GLN G 48 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS J 36 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.097812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067881 restraints weight = 73123.327| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.05 r_work: 0.3129 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25188 Z= 0.156 Angle : 0.597 10.276 35064 Z= 0.297 Chirality : 0.039 0.231 4160 Planarity : 0.004 0.046 3692 Dihedral : 18.273 173.181 5975 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.09 % Allowed : 29.32 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2481 helix: 1.44 (0.17), residues: 975 sheet: 0.53 (0.23), residues: 496 loop : -1.52 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 47 TYR 0.015 0.001 TYR B 300 PHE 0.019 0.001 PHE D 191 TRP 0.038 0.001 TRP F 106 HIS 0.006 0.001 HIS L 132 Details of bonding type rmsd covalent geometry : bond 0.00347 (25188) covalent geometry : angle 0.59736 (35064) hydrogen bonds : bond 0.04430 ( 921) hydrogen bonds : angle 4.39444 ( 2637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 220 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7431 (t80) REVERT: B 513 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8891 (mtm180) REVERT: B 720 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7762 (pp30) REVERT: B 849 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9094 (mt) REVERT: B 851 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7550 (t-90) REVERT: D 42 MET cc_start: 0.6936 (mmm) cc_final: 0.6288 (mtp) REVERT: D 187 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 118 ASN cc_start: 0.9352 (m-40) cc_final: 0.8865 (m-40) REVERT: F 50 MET cc_start: 0.6873 (ptm) cc_final: 0.6593 (ptm) REVERT: G 110 GLU cc_start: 0.7616 (mp0) cc_final: 0.6987 (mp0) REVERT: G 112 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8537 (mt-10) REVERT: I 58 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8388 (t80) REVERT: I 126 CYS cc_start: 0.9197 (m) cc_final: 0.8633 (t) REVERT: J 58 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7959 (t80) REVERT: M 56 GLN cc_start: 0.8531 (mp10) cc_final: 0.8322 (tm-30) REVERT: M 70 TYR cc_start: 0.8549 (t80) cc_final: 0.8202 (t80) REVERT: M 216 TYR cc_start: 0.6038 (t80) cc_final: 0.5809 (t80) outliers start: 112 outliers final: 38 residues processed: 304 average time/residue: 0.6049 time to fit residues: 212.3237 Evaluate side-chains 238 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 194 MET Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 234 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 HIS ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 111 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN L 255 ASN ** M 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.093249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062894 restraints weight = 73042.539| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.02 r_work: 0.3015 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25188 Z= 0.227 Angle : 0.651 13.440 35064 Z= 0.324 Chirality : 0.041 0.255 4160 Planarity : 0.005 0.043 3692 Dihedral : 18.213 175.359 5970 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.18 % Allowed : 28.32 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2481 helix: 1.41 (0.17), residues: 990 sheet: 0.55 (0.23), residues: 485 loop : -1.60 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 198 TYR 0.012 0.002 TYR D 150 PHE 0.018 0.002 PHE L 44 TRP 0.024 0.002 TRP M 184 HIS 0.008 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00514 (25188) covalent geometry : angle 0.65093 (35064) hydrogen bonds : bond 0.04976 ( 921) hydrogen bonds : angle 4.44482 ( 2637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 206 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7873 (ptp-170) REVERT: B 146 HIS cc_start: 0.7538 (m90) cc_final: 0.6999 (t-90) REVERT: B 411 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7316 (t80) REVERT: B 513 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8899 (mtm180) REVERT: B 849 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9144 (mt) REVERT: D 42 MET cc_start: 0.7270 (mmm) cc_final: 0.6951 (mtp) REVERT: E 35 ASP cc_start: 0.9102 (t0) cc_final: 0.8811 (m-30) REVERT: F 50 MET cc_start: 0.6810 (ptm) cc_final: 0.6537 (ptm) REVERT: G 44 ASP cc_start: 0.8111 (t0) cc_final: 0.7895 (t0) REVERT: G 110 GLU cc_start: 0.7837 (mp0) cc_final: 0.7293 (mp0) REVERT: G 112 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8583 (mt-10) REVERT: H 49 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8492 (tptp) REVERT: H 120 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: I 58 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8641 (t80) REVERT: I 109 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8390 (p) REVERT: I 123 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: I 127 ILE cc_start: 0.9553 (OUTLIER) cc_final: 0.9280 (mp) REVERT: J 58 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7996 (t80) REVERT: K 23 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8289 (ptp-170) REVERT: L 105 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8104 (m110) REVERT: M 51 LEU cc_start: 0.9521 (mm) cc_final: 0.9274 (pp) REVERT: M 56 GLN cc_start: 0.8587 (mp10) cc_final: 0.8271 (tm-30) REVERT: M 70 TYR cc_start: 0.8454 (t80) cc_final: 0.8126 (t80) REVERT: M 71 SER cc_start: 0.9074 (m) cc_final: 0.8862 (p) REVERT: M 75 ARG cc_start: 0.9078 (mtp85) cc_final: 0.7992 (ttm-80) REVERT: M 105 GLN cc_start: 0.8798 (mm110) cc_final: 0.8585 (mp10) REVERT: M 187 TYR cc_start: 0.9019 (m-80) cc_final: 0.8648 (m-80) REVERT: M 232 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8268 (tp-100) outliers start: 136 outliers final: 51 residues processed: 315 average time/residue: 0.5704 time to fit residues: 208.4968 Evaluate side-chains 246 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 993 MET Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 143 CYS Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 234 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 50 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 229 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 218 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 82 optimal weight: 0.0050 chunk 228 optimal weight: 6.9990 chunk 148 optimal weight: 0.4980 overall best weight: 2.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 59 ASN E 111 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.092886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062633 restraints weight = 72836.189| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.06 r_work: 0.3015 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25188 Z= 0.176 Angle : 0.603 12.634 35064 Z= 0.298 Chirality : 0.040 0.205 4160 Planarity : 0.004 0.041 3692 Dihedral : 18.203 175.326 5968 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.18 % Allowed : 29.23 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2481 helix: 1.55 (0.17), residues: 989 sheet: 0.52 (0.23), residues: 486 loop : -1.59 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.022 0.001 TYR D 109 PHE 0.016 0.001 PHE L 44 TRP 0.025 0.001 TRP M 184 HIS 0.006 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00395 (25188) covalent geometry : angle 0.60259 (35064) hydrogen bonds : bond 0.04194 ( 921) hydrogen bonds : angle 4.30279 ( 2637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 205 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 513 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8917 (mtm180) REVERT: B 849 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9136 (mt) REVERT: D 42 MET cc_start: 0.7366 (mmm) cc_final: 0.6992 (mtp) REVERT: D 90 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8926 (ptpp) REVERT: E 35 ASP cc_start: 0.9073 (t0) cc_final: 0.8803 (m-30) REVERT: F 38 MET cc_start: 0.8637 (mmm) cc_final: 0.8340 (tpp) REVERT: F 50 MET cc_start: 0.6925 (ptm) cc_final: 0.6587 (ptm) REVERT: F 126 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6539 (pp) REVERT: F 130 LYS cc_start: 0.7045 (ttpp) cc_final: 0.6609 (tppt) REVERT: G 44 ASP cc_start: 0.8082 (t0) cc_final: 0.7830 (t0) REVERT: G 110 GLU cc_start: 0.7892 (mp0) cc_final: 0.7495 (mp0) REVERT: G 112 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8613 (mt-10) REVERT: H 49 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8528 (tptp) REVERT: I 58 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8531 (t80) REVERT: I 109 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8381 (p) REVERT: I 123 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: I 130 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8859 (t) REVERT: J 58 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8085 (t80) REVERT: J 109 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8716 (p) REVERT: L 105 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8083 (m110) REVERT: M 51 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9203 (pp) REVERT: M 56 GLN cc_start: 0.8617 (mp10) cc_final: 0.8246 (tm-30) REVERT: M 70 TYR cc_start: 0.8489 (t80) cc_final: 0.7798 (t80) REVERT: M 71 SER cc_start: 0.9113 (m) cc_final: 0.8903 (p) REVERT: M 187 TYR cc_start: 0.9008 (m-80) cc_final: 0.8566 (m-80) REVERT: M 232 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8290 (tp-100) outliers start: 114 outliers final: 44 residues processed: 299 average time/residue: 0.5733 time to fit residues: 199.9767 Evaluate side-chains 249 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 993 MET Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 143 CYS Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 227 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.0070 chunk 204 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 59 ASN G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.091557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061301 restraints weight = 72801.691| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.00 r_work: 0.2985 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25188 Z= 0.214 Angle : 0.623 12.712 35064 Z= 0.310 Chirality : 0.040 0.217 4160 Planarity : 0.004 0.062 3692 Dihedral : 18.231 175.537 5966 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.95 % Allowed : 29.27 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2481 helix: 1.57 (0.17), residues: 987 sheet: 0.56 (0.23), residues: 497 loop : -1.65 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 16 TYR 0.014 0.002 TYR H 19 PHE 0.017 0.001 PHE G 93 TRP 0.027 0.002 TRP M 184 HIS 0.007 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00485 (25188) covalent geometry : angle 0.62320 (35064) hydrogen bonds : bond 0.04467 ( 921) hydrogen bonds : angle 4.36140 ( 2637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 198 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6909 (ptp-170) REVERT: B 411 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 513 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8910 (mtm180) REVERT: B 849 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9168 (mt) REVERT: D 171 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8301 (pp20) REVERT: D 172 ASP cc_start: 0.8110 (p0) cc_final: 0.7795 (p0) REVERT: E 35 ASP cc_start: 0.9094 (t0) cc_final: 0.8819 (m-30) REVERT: F 37 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8566 (OUTLIER) REVERT: F 50 MET cc_start: 0.6841 (ptm) cc_final: 0.6539 (ptm) REVERT: F 126 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6575 (pp) REVERT: F 130 LYS cc_start: 0.7275 (ttpp) cc_final: 0.6851 (ttpt) REVERT: G 44 ASP cc_start: 0.8131 (t0) cc_final: 0.7884 (t0) REVERT: G 110 GLU cc_start: 0.7963 (mp0) cc_final: 0.7553 (mp0) REVERT: G 112 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8582 (mt-10) REVERT: H 49 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8489 (tptp) REVERT: I 58 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8605 (t80) REVERT: I 123 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: I 127 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9281 (mp) REVERT: I 130 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8977 (t) REVERT: J 58 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8160 (t80) REVERT: J 109 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8690 (p) REVERT: L 105 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8104 (m110) REVERT: L 126 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: M 51 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9223 (pp) REVERT: M 56 GLN cc_start: 0.8612 (mp10) cc_final: 0.8249 (tm-30) REVERT: M 70 TYR cc_start: 0.8422 (t80) cc_final: 0.7732 (t80) REVERT: M 71 SER cc_start: 0.9110 (m) cc_final: 0.8903 (p) REVERT: M 187 TYR cc_start: 0.9004 (m-80) cc_final: 0.8637 (m-80) REVERT: M 196 LEU cc_start: 0.9348 (mt) cc_final: 0.9010 (tp) REVERT: M 232 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8338 (tp-100) outliers start: 131 outliers final: 59 residues processed: 306 average time/residue: 0.5551 time to fit residues: 198.1722 Evaluate side-chains 264 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 189 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 993 MET Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 143 CYS Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 22 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 246 optimal weight: 0.0070 chunk 11 optimal weight: 30.0000 chunk 218 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN D 181 ASN E 59 ASN E 92 HIS E 111 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 53 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.092403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062416 restraints weight = 72590.056| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.01 r_work: 0.3013 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25188 Z= 0.134 Angle : 0.598 13.708 35064 Z= 0.295 Chirality : 0.039 0.253 4160 Planarity : 0.004 0.065 3692 Dihedral : 18.210 175.099 5966 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.68 % Allowed : 30.50 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2481 helix: 1.70 (0.17), residues: 973 sheet: 0.57 (0.23), residues: 489 loop : -1.54 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG M 16 TYR 0.012 0.001 TYR E 74 PHE 0.016 0.001 PHE L 44 TRP 0.031 0.001 TRP B 890 HIS 0.006 0.001 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00304 (25188) covalent geometry : angle 0.59752 (35064) hydrogen bonds : bond 0.03858 ( 921) hydrogen bonds : angle 4.22585 ( 2637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 202 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6921 (ptp-170) REVERT: B 146 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.6951 (t70) REVERT: B 411 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B 513 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8857 (mtm180) REVERT: B 849 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9140 (mt) REVERT: D 42 MET cc_start: 0.7745 (mtm) cc_final: 0.6927 (mtp) REVERT: D 171 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: E 35 ASP cc_start: 0.9019 (t0) cc_final: 0.8779 (m-30) REVERT: F 38 MET cc_start: 0.8573 (tpp) cc_final: 0.8325 (tpp) REVERT: F 50 MET cc_start: 0.6750 (ptm) cc_final: 0.6417 (ptm) REVERT: F 126 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6602 (pp) REVERT: F 130 LYS cc_start: 0.7289 (ttpp) cc_final: 0.6914 (tppt) REVERT: G 110 GLU cc_start: 0.7930 (mp0) cc_final: 0.7570 (mp0) REVERT: G 112 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8582 (mt-10) REVERT: H 49 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8386 (tptp) REVERT: I 58 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8599 (t80) REVERT: I 109 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8322 (p) REVERT: I 130 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8971 (t) REVERT: J 8 ASP cc_start: 0.8254 (t0) cc_final: 0.7966 (t70) REVERT: J 58 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8124 (t80) REVERT: J 109 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8679 (p) REVERT: L 105 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8107 (m110) REVERT: L 126 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: M 51 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9211 (pp) REVERT: M 70 TYR cc_start: 0.8500 (t80) cc_final: 0.7821 (t80) REVERT: M 196 LEU cc_start: 0.9335 (mt) cc_final: 0.9017 (tp) REVERT: M 232 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8375 (tp-100) outliers start: 103 outliers final: 47 residues processed: 289 average time/residue: 0.5825 time to fit residues: 196.3138 Evaluate side-chains 254 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 34 GLN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 247 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 92 HIS G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.091466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061321 restraints weight = 72646.460| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.02 r_work: 0.2988 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25188 Z= 0.183 Angle : 0.627 14.154 35064 Z= 0.310 Chirality : 0.040 0.248 4160 Planarity : 0.004 0.078 3692 Dihedral : 18.222 175.466 5966 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.59 % Allowed : 31.05 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2481 helix: 1.64 (0.17), residues: 974 sheet: 0.55 (0.23), residues: 489 loop : -1.55 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG M 16 TYR 0.024 0.001 TYR E 94 PHE 0.016 0.001 PHE L 44 TRP 0.037 0.002 TRP B 890 HIS 0.005 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00417 (25188) covalent geometry : angle 0.62676 (35064) hydrogen bonds : bond 0.04141 ( 921) hydrogen bonds : angle 4.26362 ( 2637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 197 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6847 (ptp-170) REVERT: B 146 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.6921 (t70) REVERT: B 411 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7417 (t80) REVERT: B 513 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8880 (mtm180) REVERT: B 849 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9143 (mt) REVERT: D 42 MET cc_start: 0.7773 (mtm) cc_final: 0.7011 (mtp) REVERT: D 171 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8227 (pp20) REVERT: D 172 ASP cc_start: 0.8215 (p0) cc_final: 0.7810 (p0) REVERT: E 35 ASP cc_start: 0.9045 (t0) cc_final: 0.8806 (m-30) REVERT: E 144 ARG cc_start: 0.7158 (ptm-80) cc_final: 0.6936 (ptm-80) REVERT: F 37 HIS cc_start: 0.8829 (t-90) cc_final: 0.8610 (t70) REVERT: F 38 MET cc_start: 0.8587 (tpp) cc_final: 0.8313 (tpp) REVERT: F 50 MET cc_start: 0.6985 (ptm) cc_final: 0.6622 (ptm) REVERT: F 126 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6622 (pp) REVERT: F 130 LYS cc_start: 0.7344 (ttpp) cc_final: 0.6967 (tppt) REVERT: G 53 GLN cc_start: 0.9137 (tp40) cc_final: 0.8639 (mm-40) REVERT: G 110 GLU cc_start: 0.8012 (mp0) cc_final: 0.7629 (mp0) REVERT: G 112 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8566 (mt-10) REVERT: H 29 GLN cc_start: 0.8717 (pp30) cc_final: 0.8301 (pp30) REVERT: H 49 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8433 (tptp) REVERT: I 58 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8620 (t80) REVERT: I 127 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9305 (mp) REVERT: I 233 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8700 (pp20) REVERT: J 8 ASP cc_start: 0.8231 (t0) cc_final: 0.7995 (t70) REVERT: J 58 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8172 (t80) REVERT: J 109 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8686 (p) REVERT: L 105 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8126 (m110) REVERT: L 126 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8278 (mm-30) REVERT: M 51 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9206 (pp) REVERT: M 70 TYR cc_start: 0.8474 (t80) cc_final: 0.7829 (t80) REVERT: M 75 ARG cc_start: 0.8981 (mtm180) cc_final: 0.8779 (mtp85) REVERT: M 187 TYR cc_start: 0.9088 (m-80) cc_final: 0.8732 (m-80) REVERT: M 196 LEU cc_start: 0.9333 (mt) cc_final: 0.9026 (tp) REVERT: M 232 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8348 (tp-100) outliers start: 101 outliers final: 55 residues processed: 280 average time/residue: 0.5520 time to fit residues: 180.2675 Evaluate side-chains 262 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 191 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 143 CYS Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 260 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 222 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 92 HIS E 111 GLN E 128 ASN G 48 GLN G 53 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.092467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062432 restraints weight = 72301.258| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.02 r_work: 0.3016 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25188 Z= 0.119 Angle : 0.598 14.523 35064 Z= 0.295 Chirality : 0.039 0.257 4160 Planarity : 0.004 0.081 3692 Dihedral : 18.213 175.028 5966 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.77 % Allowed : 31.95 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2481 helix: 1.71 (0.17), residues: 970 sheet: 0.56 (0.23), residues: 491 loop : -1.48 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG M 16 TYR 0.014 0.001 TYR K 24 PHE 0.016 0.001 PHE L 44 TRP 0.042 0.001 TRP B 890 HIS 0.009 0.001 HIS H 20 Details of bonding type rmsd covalent geometry : bond 0.00272 (25188) covalent geometry : angle 0.59773 (35064) hydrogen bonds : bond 0.03672 ( 921) hydrogen bonds : angle 4.16032 ( 2637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 198 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.6824 (t70) REVERT: B 411 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 513 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8843 (mtm180) REVERT: B 849 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9134 (mt) REVERT: D 42 MET cc_start: 0.7839 (mtm) cc_final: 0.7047 (mtp) REVERT: D 171 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8005 (pp20) REVERT: E 35 ASP cc_start: 0.8999 (t0) cc_final: 0.8775 (m-30) REVERT: F 38 MET cc_start: 0.8643 (tpp) cc_final: 0.8308 (tpp) REVERT: F 50 MET cc_start: 0.6961 (ptm) cc_final: 0.6567 (ptm) REVERT: F 104 GLU cc_start: 0.6342 (tp30) cc_final: 0.5878 (mp0) REVERT: F 126 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6576 (pp) REVERT: G 53 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8672 (tp-100) REVERT: G 57 ASP cc_start: 0.8760 (m-30) cc_final: 0.8178 (m-30) REVERT: G 110 GLU cc_start: 0.7984 (mp0) cc_final: 0.7637 (mp0) REVERT: G 112 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8584 (mt-10) REVERT: H 49 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8347 (tptp) REVERT: I 58 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8508 (t80) REVERT: I 109 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8305 (p) REVERT: I 127 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9302 (mp) REVERT: J 8 ASP cc_start: 0.8115 (t0) cc_final: 0.7908 (t70) REVERT: J 58 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (t80) REVERT: J 109 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8666 (p) REVERT: L 105 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8110 (m110) REVERT: L 126 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: M 51 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9181 (pp) REVERT: M 70 TYR cc_start: 0.8455 (t80) cc_final: 0.7802 (t80) REVERT: M 75 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8703 (mtp85) REVERT: M 187 TYR cc_start: 0.9064 (m-80) cc_final: 0.8718 (m-80) REVERT: M 196 LEU cc_start: 0.9342 (mt) cc_final: 0.9022 (tp) REVERT: M 232 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8356 (tp-100) outliers start: 83 outliers final: 43 residues processed: 268 average time/residue: 0.5808 time to fit residues: 180.8872 Evaluate side-chains 248 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 198 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 92 HIS G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060963 restraints weight = 72893.372| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.05 r_work: 0.2983 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25188 Z= 0.193 Angle : 0.647 14.533 35064 Z= 0.319 Chirality : 0.040 0.248 4160 Planarity : 0.005 0.092 3692 Dihedral : 18.233 175.654 5966 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.95 % Allowed : 32.00 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2481 helix: 1.62 (0.17), residues: 975 sheet: 0.55 (0.23), residues: 489 loop : -1.53 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 16 TYR 0.015 0.001 TYR E 86 PHE 0.016 0.001 PHE L 44 TRP 0.051 0.002 TRP B 890 HIS 0.020 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00442 (25188) covalent geometry : angle 0.64695 (35064) hydrogen bonds : bond 0.04157 ( 921) hydrogen bonds : angle 4.25332 ( 2637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 197 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6881 (ptp-170) REVERT: B 146 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.6900 (t70) REVERT: B 411 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7395 (t80) REVERT: B 513 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8873 (mtm180) REVERT: B 849 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9149 (mt) REVERT: D 171 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8214 (pp20) REVERT: D 172 ASP cc_start: 0.8178 (p0) cc_final: 0.7796 (p0) REVERT: E 35 ASP cc_start: 0.9047 (t0) cc_final: 0.8806 (m-30) REVERT: F 38 MET cc_start: 0.8608 (tpp) cc_final: 0.8363 (tpp) REVERT: F 50 MET cc_start: 0.6910 (ptm) cc_final: 0.6515 (ptm) REVERT: F 104 GLU cc_start: 0.6333 (tp30) cc_final: 0.5906 (mp0) REVERT: F 126 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6597 (pp) REVERT: G 57 ASP cc_start: 0.8684 (m-30) cc_final: 0.8406 (m-30) REVERT: G 110 GLU cc_start: 0.8043 (mp0) cc_final: 0.7682 (mp0) REVERT: G 112 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8584 (mt-10) REVERT: H 29 GLN cc_start: 0.8671 (pp30) cc_final: 0.8292 (pp30) REVERT: H 49 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8470 (tptp) REVERT: I 58 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8544 (t80) REVERT: I 127 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9321 (mp) REVERT: I 233 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8698 (pp20) REVERT: J 8 ASP cc_start: 0.8220 (t0) cc_final: 0.7972 (t70) REVERT: J 58 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8247 (t80) REVERT: J 109 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8682 (p) REVERT: L 105 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8144 (m110) REVERT: L 126 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: L 299 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8846 (m90) REVERT: M 51 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9202 (pp) REVERT: M 70 TYR cc_start: 0.8442 (t80) cc_final: 0.7731 (t80) REVERT: M 187 TYR cc_start: 0.9026 (m-80) cc_final: 0.8646 (m-80) REVERT: M 196 LEU cc_start: 0.9369 (mt) cc_final: 0.9062 (tp) REVERT: M 232 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8357 (tp-100) outliers start: 87 outliers final: 57 residues processed: 268 average time/residue: 0.5752 time to fit residues: 178.9519 Evaluate side-chains 260 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 143 CYS Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 258 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 263 optimal weight: 0.0070 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 111 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 255 ASN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.092451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062619 restraints weight = 72458.435| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.00 r_work: 0.3021 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25188 Z= 0.118 Angle : 0.626 15.207 35064 Z= 0.306 Chirality : 0.039 0.255 4160 Planarity : 0.004 0.089 3692 Dihedral : 18.237 174.953 5966 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.91 % Allowed : 33.05 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2481 helix: 1.74 (0.17), residues: 963 sheet: 0.55 (0.23), residues: 493 loop : -1.45 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG M 16 TYR 0.015 0.001 TYR K 24 PHE 0.017 0.001 PHE L 44 TRP 0.060 0.001 TRP B 890 HIS 0.007 0.001 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00274 (25188) covalent geometry : angle 0.62631 (35064) hydrogen bonds : bond 0.03601 ( 921) hydrogen bonds : angle 4.16656 ( 2637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6430 (t70) REVERT: B 411 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7359 (t80) REVERT: B 513 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8776 (mtm180) REVERT: B 849 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9133 (mt) REVERT: D 171 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7962 (pp20) REVERT: E 35 ASP cc_start: 0.8989 (t0) cc_final: 0.8770 (m-30) REVERT: F 37 HIS cc_start: 0.8764 (t-90) cc_final: 0.8564 (t70) REVERT: F 38 MET cc_start: 0.8536 (tpp) cc_final: 0.8285 (tpp) REVERT: F 50 MET cc_start: 0.6878 (ptm) cc_final: 0.6464 (ptm) REVERT: F 57 MET cc_start: 0.8892 (tmm) cc_final: 0.8266 (ppp) REVERT: F 104 GLU cc_start: 0.6416 (tp30) cc_final: 0.6037 (mp0) REVERT: F 126 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6650 (pp) REVERT: G 110 GLU cc_start: 0.7960 (mp0) cc_final: 0.7628 (mp0) REVERT: H 29 GLN cc_start: 0.8673 (pp30) cc_final: 0.8248 (pp30) REVERT: I 58 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8501 (t80) REVERT: I 109 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8270 (p) REVERT: I 127 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9315 (mp) REVERT: J 8 ASP cc_start: 0.8088 (t0) cc_final: 0.7883 (t70) REVERT: J 58 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8176 (t80) REVERT: J 109 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8659 (p) REVERT: L 105 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8112 (m110) REVERT: L 126 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: L 299 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8805 (m90) REVERT: M 51 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9164 (pp) REVERT: M 70 TYR cc_start: 0.8451 (t80) cc_final: 0.7741 (t80) REVERT: M 75 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8727 (mtm110) REVERT: M 187 TYR cc_start: 0.9047 (m-80) cc_final: 0.8687 (m-80) REVERT: M 196 LEU cc_start: 0.9356 (mt) cc_final: 0.9054 (tp) REVERT: M 232 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8338 (tp-100) outliers start: 64 outliers final: 38 residues processed: 246 average time/residue: 0.5903 time to fit residues: 168.8184 Evaluate side-chains 239 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 298 CYS Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 54 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN G 48 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.091586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061470 restraints weight = 72961.858| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.05 r_work: 0.2994 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25188 Z= 0.160 Angle : 0.640 14.767 35064 Z= 0.315 Chirality : 0.040 0.227 4160 Planarity : 0.004 0.091 3692 Dihedral : 18.229 175.501 5966 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.09 % Allowed : 33.14 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2481 helix: 1.70 (0.17), residues: 972 sheet: 0.54 (0.23), residues: 492 loop : -1.48 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG M 16 TYR 0.026 0.001 TYR D 109 PHE 0.016 0.001 PHE L 44 TRP 0.047 0.002 TRP B 890 HIS 0.008 0.001 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00371 (25188) covalent geometry : angle 0.63990 (35064) hydrogen bonds : bond 0.03909 ( 921) hydrogen bonds : angle 4.20327 ( 2637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9708.28 seconds wall clock time: 165 minutes 45.46 seconds (9945.46 seconds total)