Starting phenix.real_space_refine on Fri Dec 27 17:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa6_38195/12_2024/8xa6_38195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa6_38195/12_2024/8xa6_38195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa6_38195/12_2024/8xa6_38195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa6_38195/12_2024/8xa6_38195.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa6_38195/12_2024/8xa6_38195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa6_38195/12_2024/8xa6_38195.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 S 87 5.16 5 C 15306 2.51 5 N 4225 2.21 5 O 4658 1.98 5 H 24502 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48778 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3456 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3456 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain: "C" Number of atoms: 17931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 17931 Classifications: {'peptide': 1139} Link IDs: {'PTRANS': 54, 'TRANS': 1084} Chain breaks: 1 Chain: "D" Number of atoms: 18775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 18775 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 1 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 990 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "L" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1503 Classifications: {'peptide': 92} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "E" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1113 Classifications: {'peptide': 69} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1554 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'CIS': 2, 'TRANS': 91} Time building chain proxies: 16.33, per 1000 atoms: 0.33 Number of scatterers: 48778 At special positions: 0 Unit cell: (133, 152.95, 176.7, 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 87 16.00 O 4658 8.00 N 4225 7.00 C 15306 6.00 H 24502 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 78 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5686 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 36 sheets defined 35.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.775A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.511A pdb=" N ALA A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.606A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.919A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 85 removed outlier: 4.258A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.507A pdb=" N LYS B 155 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 227 removed outlier: 4.410A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.667A pdb=" N GLU C 43 " --> pdb=" O TRP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 191 through 198 removed outlier: 4.039A pdb=" N LEU C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.886A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 268 through 279 removed outlier: 3.915A pdb=" N ARG C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 377 through 394 removed outlier: 3.851A pdb=" N ILE C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 439 removed outlier: 4.234A pdb=" N ARG C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 removed outlier: 4.164A pdb=" N GLN C 447 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 449 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 507 through 511 Processing helix chain 'C' and resid 565 through 571 removed outlier: 4.507A pdb=" N ASN C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 633 through 646 Processing helix chain 'C' and resid 661 through 669 removed outlier: 4.322A pdb=" N VAL C 665 " --> pdb=" O GLY C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.547A pdb=" N PHE C 865 " --> pdb=" O HIS C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 965 removed outlier: 4.081A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 984 removed outlier: 4.052A pdb=" N VAL C 971 " --> pdb=" O ASN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'C' and resid 1076 through 1086 Processing helix chain 'C' and resid 1088 through 1098 Processing helix chain 'C' and resid 1102 through 1116 removed outlier: 3.510A pdb=" N ARG C1106 " --> pdb=" O ASP C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1138 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.812A pdb=" N ILE D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.920A pdb=" N GLU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 172 through 179 removed outlier: 4.026A pdb=" N HIS D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 179 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 200 through 219 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.991A pdb=" N ILE D 227 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 270 removed outlier: 4.292A pdb=" N ARG D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS D 269 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 297 removed outlier: 4.283A pdb=" N GLN D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 removed outlier: 4.001A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.645A pdb=" N GLN D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.801A pdb=" N GLU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 378 removed outlier: 3.658A pdb=" N VAL D 370 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.577A pdb=" N ASP D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.619A pdb=" N CYS D 443 " --> pdb=" O PRO D 440 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 444 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'D' and resid 495 through 502 Processing helix chain 'D' and resid 518 through 529 removed outlier: 3.612A pdb=" N ALA D 522 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 569 Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 601 through 609 removed outlier: 3.563A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 631 removed outlier: 3.705A pdb=" N LEU D 620 " --> pdb=" O LYS D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 653 Processing helix chain 'D' and resid 659 through 664 removed outlier: 3.633A pdb=" N VAL D 664 " --> pdb=" O SER D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.703A pdb=" N GLN D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 690 removed outlier: 3.864A pdb=" N ASP D 681 " --> pdb=" O GLN D 677 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN D 682 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 683 " --> pdb=" O LYS D 679 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET D 684 " --> pdb=" O VAL D 680 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 685 " --> pdb=" O ASP D 681 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D 686 " --> pdb=" O ASN D 682 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 687 " --> pdb=" O VAL D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 720 Processing helix chain 'D' and resid 724 through 733 Processing helix chain 'D' and resid 737 through 746 Processing helix chain 'D' and resid 772 through 808 removed outlier: 3.839A pdb=" N GLY D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 843 Processing helix chain 'D' and resid 869 through 878 removed outlier: 3.668A pdb=" N ALA D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 918 through 929 Processing helix chain 'D' and resid 930 through 932 No H-bonds generated for 'chain 'D' and resid 930 through 932' Processing helix chain 'D' and resid 952 through 961 Processing helix chain 'D' and resid 1030 through 1038 Processing helix chain 'D' and resid 1039 through 1059 removed outlier: 3.686A pdb=" N VAL D1043 " --> pdb=" O ASP D1039 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR D1055 " --> pdb=" O VAL D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1073 removed outlier: 3.760A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1076 No H-bonds generated for 'chain 'D' and resid 1074 through 1076' Processing helix chain 'D' and resid 1095 through 1108 Processing helix chain 'D' and resid 1122 through 1128 removed outlier: 4.149A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1153 Processing helix chain 'D' and resid 1160 through 1168 removed outlier: 3.525A pdb=" N ASN D1164 " --> pdb=" O GLY D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1182 removed outlier: 3.689A pdb=" N MET D1177 " --> pdb=" O GLY D1174 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N MET D1178 " --> pdb=" O THR D1175 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS D1179 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D1182 " --> pdb=" O LYS D1179 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 11 Processing helix chain 'F' and resid 15 through 34 Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.588A pdb=" N ASP F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 14 removed outlier: 3.802A pdb=" N GLU L 13 " --> pdb=" O GLU L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 27 removed outlier: 3.969A pdb=" N GLU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS L 27 " --> pdb=" O LEU L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 22 through 27' Processing helix chain 'L' and resid 33 through 42 Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 54 through 65 removed outlier: 4.567A pdb=" N ASP L 65 " --> pdb=" O ASP L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 92 removed outlier: 3.605A pdb=" N GLN L 92 " --> pdb=" O ASP L 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 37 Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 22 through 38 removed outlier: 3.788A pdb=" N ARG H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 93 removed outlier: 3.539A pdb=" N GLY H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 6.857A pdb=" N LYS A 22 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 14 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE A 20 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 185 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR A 191 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102 removed outlier: 6.318A pdb=" N GLN A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL A 53 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.756A pdb=" N SER A 168 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 4.126A pdb=" N LYS B 22 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LYS B 22 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 198 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 24 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 196 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU B 26 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 194 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 185 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 191 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.652A pdb=" N GLY B 145 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 58 removed outlier: 6.598A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE B 58 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ARG B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 8.623A pdb=" N ALA C 988 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 57 removed outlier: 4.301A pdb=" N LEU C 62 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS C 95 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR C 69 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG C 93 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 147 removed outlier: 3.815A pdb=" N SER C 143 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 350 Processing sheet with id=AB8, first strand: chain 'C' and resid 485 through 487 removed outlier: 4.486A pdb=" N SER C 530 " --> pdb=" O CYS C 515 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537 removed outlier: 5.334A pdb=" N ARG C 560 " --> pdb=" O ARG C 549 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 574 through 575 Processing sheet with id=AC2, first strand: chain 'C' and resid 592 through 595 Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 684 removed outlier: 5.470A pdb=" N VAL C 682 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG C 693 " --> pdb=" O VAL C 682 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 706 " --> pdb=" O ARG C 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AC5, first strand: chain 'C' and resid 1014 through 1015 removed outlier: 4.193A pdb=" N GLY C 927 " --> pdb=" O ASN C 931 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE C 775 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 938 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET C 777 " --> pdb=" O ILE C 938 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER C1031 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 788 through 799 removed outlier: 4.350A pdb=" N ASP C 889 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 914 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 887 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 845 through 847 removed outlier: 3.894A pdb=" N ARG C 873 " --> pdb=" O THR C 847 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.819A pdb=" N ARG C1051 " --> pdb=" O SER D 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER D 339 " --> pdb=" O ARG C1051 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AD1, first strand: chain 'C' and resid 1142 through 1143 removed outlier: 3.817A pdb=" N LYS C1143 " --> pdb=" O ASN D 11 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN D 11 " --> pdb=" O LYS C1143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 515 through 516 removed outlier: 3.750A pdb=" N PHE D 516 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 540 " --> pdb=" O PHE D 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 824 through 826 Processing sheet with id=AD4, first strand: chain 'D' and resid 829 through 831 removed outlier: 6.077A pdb=" N GLU D 831 " --> pdb=" O THR D 835 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR D 835 " --> pdb=" O GLU D 831 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 977 through 981 Processing sheet with id=AD6, first strand: chain 'D' and resid 1078 through 1080 Processing sheet with id=AD7, first strand: chain 'L' and resid 69 through 71 Processing sheet with id=AD8, first strand: chain 'E' and resid 21 through 26 Processing sheet with id=AD9, first strand: chain 'H' and resid 58 through 61 removed outlier: 5.848A pdb=" N ILE H 58 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER H 69 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR H 70 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR H 81 " --> pdb=" O TYR H 70 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2406 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.60 Time building geometry restraints manager: 10.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.13: 24488 1.13 - 1.40: 9776 1.40 - 1.67: 14751 1.67 - 1.94: 163 1.94 - 2.21: 2 Bond restraints: 49180 Sorted by residual: bond pdb=" CD2 TYR D 70 " pdb=" CE2 TYR D 70 " ideal model delta sigma weight residual 1.382 2.206 -0.824 3.00e-02 1.11e+03 7.54e+02 bond pdb=" CD1 TYR D 70 " pdb=" CE1 TYR D 70 " ideal model delta sigma weight residual 1.382 2.203 -0.821 3.00e-02 1.11e+03 7.49e+02 bond pdb=" N GLY D 79 " pdb=" CA GLY D 79 " ideal model delta sigma weight residual 1.449 1.793 -0.344 1.45e-02 4.76e+03 5.61e+02 bond pdb=" CE2 TYR D 70 " pdb=" CZ TYR D 70 " ideal model delta sigma weight residual 1.378 1.880 -0.502 2.40e-02 1.74e+03 4.37e+02 bond pdb=" CE1 TYR D 70 " pdb=" CZ TYR D 70 " ideal model delta sigma weight residual 1.378 1.846 -0.468 2.40e-02 1.74e+03 3.80e+02 ... (remaining 49175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.83: 89184 9.83 - 19.65: 2 19.65 - 29.48: 0 29.48 - 39.31: 2 39.31 - 49.14: 1 Bond angle restraints: 89189 Sorted by residual: angle pdb=" CA ARG C 312 " pdb=" N ARG C 312 " pdb=" H ARG C 312 " ideal model delta sigma weight residual 114.00 163.14 -49.14 3.00e+00 1.11e-01 2.68e+02 angle pdb=" C CYS D 78 " pdb=" N GLY D 79 " pdb=" CA GLY D 79 " ideal model delta sigma weight residual 121.41 151.91 -30.50 1.96e+00 2.60e-01 2.42e+02 angle pdb=" CA GLY D 79 " pdb=" N GLY D 79 " pdb=" H GLY D 79 " ideal model delta sigma weight residual 114.15 83.08 31.07 3.00e+00 1.11e-01 1.07e+02 angle pdb=" N GLY D 79 " pdb=" CA GLY D 79 " pdb=" C GLY D 79 " ideal model delta sigma weight residual 113.18 131.37 -18.19 2.37e+00 1.78e-01 5.89e+01 angle pdb=" CA PRO D 610 " pdb=" N PRO D 610 " pdb=" CD PRO D 610 " ideal model delta sigma weight residual 112.00 102.31 9.69 1.40e+00 5.10e-01 4.79e+01 ... (remaining 89184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 20005 17.96 - 35.93: 1969 35.93 - 53.89: 634 53.89 - 71.86: 183 71.86 - 89.82: 65 Dihedral angle restraints: 22856 sinusoidal: 12863 harmonic: 9993 Sorted by residual: dihedral pdb=" CB CYS D 62 " pdb=" SG CYS D 62 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual 93.00 148.53 -55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA CYS D 78 " pdb=" C CYS D 78 " pdb=" N GLY D 79 " pdb=" CA GLY D 79 " ideal model delta harmonic sigma weight residual -180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA GLY D 79 " pdb=" C GLY D 79 " pdb=" N VAL D 80 " pdb=" CA VAL D 80 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 22853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2787 0.038 - 0.076: 653 0.076 - 0.115: 261 0.115 - 0.153: 71 0.153 - 0.191: 2 Chirality restraints: 3774 Sorted by residual: chirality pdb=" CB ILE C 792 " pdb=" CA ILE C 792 " pdb=" CG1 ILE C 792 " pdb=" CG2 ILE C 792 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA PRO D 610 " pdb=" N PRO D 610 " pdb=" C PRO D 610 " pdb=" CB PRO D 610 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA ILE D 234 " pdb=" N ILE D 234 " pdb=" C ILE D 234 " pdb=" CB ILE D 234 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3771 not shown) Planarity restraints: 7287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 70 " 0.026 2.00e-02 2.50e+03 3.76e-02 4.24e+01 pdb=" CG TYR D 70 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 70 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 70 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR D 70 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 70 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 70 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 70 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TYR D 70 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR D 70 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR D 70 " 0.064 2.00e-02 2.50e+03 pdb=" HE2 TYR D 70 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 609 " -0.064 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO D 610 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 610 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 610 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 78 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C CYS D 78 " -0.041 2.00e-02 2.50e+03 pdb=" O CYS D 78 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY D 79 " 0.013 2.00e-02 2.50e+03 ... (remaining 7284 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 339 1.85 - 2.53: 41283 2.53 - 3.22: 142076 3.22 - 3.91: 170841 3.91 - 4.60: 261670 Nonbonded interactions: 616209 Sorted by model distance: nonbonded pdb=" CD1 TYR D 70 " pdb=" H GLY D 79 " model vdw 1.158 2.800 nonbonded pdb=" HH TYR C 664 " pdb="HD11 ILE C 741 " model vdw 1.220 2.270 nonbonded pdb=" HG SER A 47 " pdb=" HE1 TYR B 32 " model vdw 1.290 2.100 nonbonded pdb=" O VAL D 915 " pdb=" HH TYR D1180 " model vdw 1.304 2.450 nonbonded pdb="HD22 LEU C 947 " pdb=" HG1 THR C1015 " model vdw 1.328 2.270 ... (remaining 616204 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 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.670 Extract box with map and model: 1.320 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 71.990 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4755 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 : 0.010 0.824 24678 Z= 0.715 Angle : 0.611 30.500 33339 Z= 0.331 Chirality : 0.041 0.191 3774 Planarity : 0.004 0.090 4348 Dihedral : 18.050 89.822 9443 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.30 % Favored : 94.44 % Rotamer: Outliers : 0.19 % Allowed : 25.48 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3059 helix: 0.69 (0.18), residues: 933 sheet: 0.33 (0.27), residues: 349 loop : -1.54 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 199 HIS 0.004 0.001 HIS D 534 PHE 0.012 0.001 PHE C1075 TYR 0.037 0.001 TYR D 70 ARG 0.006 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.5496 (m-30) cc_final: 0.5076 (m-30) REVERT: C 131 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: D 866 GLU cc_start: 0.0903 (pm20) cc_final: -0.0972 (pm20) REVERT: H 75 MET cc_start: 0.2836 (mmt) cc_final: 0.1057 (ppp) outliers start: 5 outliers final: 4 residues processed: 208 average time/residue: 0.6545 time to fit residues: 221.0605 Evaluate side-chains 199 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain D residue 120 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4797 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.820 24678 Z= 0.718 Angle : 0.600 30.804 33339 Z= 0.309 Chirality : 0.042 0.154 3774 Planarity : 0.004 0.058 4348 Dihedral : 4.379 45.092 3385 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.88 % Favored : 93.85 % Rotamer: Outliers : 1.81 % Allowed : 23.11 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3059 helix: 0.64 (0.17), residues: 955 sheet: 0.29 (0.28), residues: 339 loop : -1.58 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 199 HIS 0.007 0.001 HIS D 781 PHE 0.012 0.001 PHE D 777 TYR 0.038 0.001 TYR D 70 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 TYR cc_start: 0.3410 (OUTLIER) cc_final: 0.2957 (m-80) REVERT: C 29 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3537 (pp) REVERT: C 121 ASP cc_start: 0.5624 (m-30) cc_final: 0.5197 (m-30) REVERT: C 131 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.4379 (tt0) REVERT: C 219 ASN cc_start: 0.5098 (t0) cc_final: 0.4474 (p0) REVERT: C 274 LYS cc_start: 0.6942 (mmmt) cc_final: 0.6726 (mmmt) REVERT: C 660 THR cc_start: 0.4509 (OUTLIER) cc_final: 0.4090 (p) REVERT: D 684 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.5076 (mtm) REVERT: F 44 HIS cc_start: 0.1698 (OUTLIER) cc_final: 0.1201 (m170) REVERT: H 75 MET cc_start: 0.2885 (mmt) cc_final: 0.1103 (ppp) outliers start: 48 outliers final: 27 residues processed: 227 average time/residue: 0.6094 time to fit residues: 222.3776 Evaluate side-chains 222 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain D residue 892 CYS Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 970 GLN D 568 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4945 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.828 24678 Z= 0.747 Angle : 0.653 30.505 33339 Z= 0.342 Chirality : 0.044 0.163 3774 Planarity : 0.005 0.062 4348 Dihedral : 4.751 60.595 3378 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.06 % Favored : 92.64 % Rotamer: Outliers : 3.35 % Allowed : 22.39 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 3059 helix: 0.24 (0.17), residues: 941 sheet: 0.11 (0.28), residues: 345 loop : -1.82 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 199 HIS 0.007 0.001 HIS D 781 PHE 0.019 0.002 PHE C 40 TYR 0.037 0.002 TYR D 70 ARG 0.010 0.001 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 202 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 VAL cc_start: 0.6181 (OUTLIER) cc_final: 0.5692 (t) REVERT: B 169 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7192 (mt) REVERT: C 29 LEU cc_start: 0.3646 (OUTLIER) cc_final: 0.3436 (pp) REVERT: C 219 ASN cc_start: 0.4856 (t0) cc_final: 0.4382 (p0) REVERT: C 274 LYS cc_start: 0.6637 (mmmt) cc_final: 0.6261 (mmmt) REVERT: C 632 ASP cc_start: 0.4961 (OUTLIER) cc_final: 0.4187 (m-30) REVERT: C 660 THR cc_start: 0.4720 (OUTLIER) cc_final: 0.4335 (p) REVERT: C 889 ASP cc_start: 0.4952 (OUTLIER) cc_final: 0.4330 (p0) REVERT: C 1015 THR cc_start: 0.5133 (OUTLIER) cc_final: 0.4423 (t) REVERT: D 170 MET cc_start: 0.3569 (tmm) cc_final: 0.3358 (tmm) REVERT: D 470 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5878 (mtp180) REVERT: D 767 PHE cc_start: 0.3882 (m-80) cc_final: 0.2901 (m-80) REVERT: D 843 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5623 (mm) REVERT: D 866 GLU cc_start: 0.0915 (pm20) cc_final: 0.0021 (pm20) REVERT: F 37 MET cc_start: -0.1695 (mpp) cc_final: -0.2145 (mpp) REVERT: F 44 HIS cc_start: 0.2161 (OUTLIER) cc_final: 0.0969 (m90) REVERT: L 14 MET cc_start: 0.0229 (ppp) cc_final: -0.0065 (ppp) REVERT: H 75 MET cc_start: 0.2814 (mmt) cc_final: 0.1328 (ppp) outliers start: 89 outliers final: 55 residues processed: 271 average time/residue: 0.6106 time to fit residues: 266.0002 Evaluate side-chains 258 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 623 ILE Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain D residue 892 CYS Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.5980 chunk 207 optimal weight: 0.0770 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4856 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.824 24678 Z= 0.708 Angle : 0.555 30.647 33339 Z= 0.287 Chirality : 0.041 0.152 3774 Planarity : 0.004 0.060 4348 Dihedral : 4.433 59.693 3378 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 2.15 % Allowed : 23.29 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3059 helix: 0.54 (0.17), residues: 948 sheet: 0.08 (0.28), residues: 341 loop : -1.67 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 766 HIS 0.005 0.001 HIS B 220 PHE 0.011 0.001 PHE A 136 TYR 0.037 0.001 TYR D 70 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.5792 (m-30) cc_final: 0.5411 (m-30) REVERT: C 219 ASN cc_start: 0.4572 (t0) cc_final: 0.4352 (p0) REVERT: C 274 LYS cc_start: 0.6548 (mmmt) cc_final: 0.5973 (mmmt) REVERT: C 889 ASP cc_start: 0.4819 (OUTLIER) cc_final: 0.4548 (p0) REVERT: D 684 MET cc_start: 0.5451 (mtp) cc_final: 0.5139 (mtm) REVERT: D 767 PHE cc_start: 0.3993 (m-80) cc_final: 0.2911 (m-80) REVERT: D 843 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5464 (mm) REVERT: D 936 MET cc_start: 0.2222 (mpp) cc_final: 0.0686 (ppp) REVERT: F 37 MET cc_start: -0.1594 (mpp) cc_final: -0.1991 (mpp) REVERT: F 44 HIS cc_start: 0.2029 (OUTLIER) cc_final: 0.1255 (m170) REVERT: L 14 MET cc_start: -0.0021 (ppp) cc_final: -0.0293 (ppp) REVERT: H 75 MET cc_start: 0.2806 (mmt) cc_final: 0.1248 (ppp) outliers start: 57 outliers final: 45 residues processed: 242 average time/residue: 0.6044 time to fit residues: 237.7553 Evaluate side-chains 242 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 723 CYS Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 HIS Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain D residue 892 CYS Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN C 931 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4936 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.825 24678 Z= 0.726 Angle : 0.588 30.523 33339 Z= 0.306 Chirality : 0.042 0.155 3774 Planarity : 0.004 0.060 4348 Dihedral : 4.549 60.339 3378 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.32 % Favored : 92.42 % Rotamer: Outliers : 2.83 % Allowed : 22.50 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3059 helix: 0.46 (0.17), residues: 949 sheet: -0.00 (0.28), residues: 349 loop : -1.75 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 199 HIS 0.004 0.001 HIS C 507 PHE 0.014 0.001 PHE C 40 TYR 0.037 0.002 TYR D 70 ARG 0.004 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 VAL cc_start: 0.6158 (OUTLIER) cc_final: 0.5662 (t) REVERT: B 169 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7188 (mt) REVERT: C 39 TRP cc_start: 0.6454 (OUTLIER) cc_final: 0.6212 (t60) REVERT: C 274 LYS cc_start: 0.6552 (mmmt) cc_final: 0.5920 (mmmt) REVERT: C 403 HIS cc_start: 0.6380 (OUTLIER) cc_final: 0.5834 (t-90) REVERT: C 660 THR cc_start: 0.4831 (OUTLIER) cc_final: 0.4473 (p) REVERT: C 889 ASP cc_start: 0.4914 (OUTLIER) cc_final: 0.4453 (p0) REVERT: C 1015 THR cc_start: 0.5199 (OUTLIER) cc_final: 0.4448 (t) REVERT: C 1074 ARG cc_start: 0.5307 (mtm-85) cc_final: 0.4307 (ttt90) REVERT: D 539 VAL cc_start: 0.3954 (p) cc_final: 0.3728 (p) REVERT: D 684 MET cc_start: 0.5310 (mtp) cc_final: 0.4888 (mtm) REVERT: D 843 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5576 (mm) REVERT: D 866 GLU cc_start: 0.0530 (pm20) cc_final: -0.0421 (pm20) REVERT: F 37 MET cc_start: -0.1484 (mpp) cc_final: -0.1875 (mpp) REVERT: F 44 HIS cc_start: 0.2293 (OUTLIER) cc_final: 0.1065 (m90) REVERT: L 14 MET cc_start: 0.0105 (ppp) cc_final: -0.0223 (ppp) REVERT: H 75 MET cc_start: 0.2888 (mmt) cc_final: 0.1416 (ppp) outliers start: 75 outliers final: 56 residues processed: 268 average time/residue: 0.6340 time to fit residues: 269.9373 Evaluate side-chains 263 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 723 CYS Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 778 SER Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 HIS Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain D residue 892 CYS Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 294 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 136 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN C1136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.826 24678 Z= 0.719 Angle : 0.575 30.755 33339 Z= 0.299 Chirality : 0.042 0.156 3774 Planarity : 0.004 0.066 4348 Dihedral : 4.552 62.423 3378 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.24 % Favored : 93.49 % Rotamer: Outliers : 3.35 % Allowed : 22.39 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3059 helix: 0.47 (0.17), residues: 950 sheet: 0.13 (0.29), residues: 324 loop : -1.75 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 199 HIS 0.005 0.001 HIS C 507 PHE 0.011 0.001 PHE C1128 TYR 0.037 0.002 TYR D 70 ARG 0.021 0.000 ARG D1079 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 201 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7210 (mt) REVERT: C 31 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.4054 (pm20) REVERT: C 39 TRP cc_start: 0.6348 (OUTLIER) cc_final: 0.6069 (t60) REVERT: C 274 LYS cc_start: 0.6472 (mmmt) cc_final: 0.5845 (mmmt) REVERT: C 403 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5578 (t-90) REVERT: C 660 THR cc_start: 0.4803 (OUTLIER) cc_final: 0.4466 (p) REVERT: C 696 GLU cc_start: 0.4781 (mm-30) cc_final: 0.4575 (mm-30) REVERT: C 889 ASP cc_start: 0.4871 (OUTLIER) cc_final: 0.4407 (p0) REVERT: C 1015 THR cc_start: 0.5201 (OUTLIER) cc_final: 0.4486 (t) REVERT: C 1074 ARG cc_start: 0.5270 (mtm-85) cc_final: 0.4260 (ttt90) REVERT: D 539 VAL cc_start: 0.3946 (p) cc_final: 0.3716 (p) REVERT: D 843 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5568 (mm) REVERT: D 866 GLU cc_start: 0.0548 (pm20) cc_final: -0.0340 (pm20) REVERT: D 936 MET cc_start: 0.2205 (mpp) cc_final: 0.0678 (ppp) REVERT: F 44 HIS cc_start: 0.2296 (OUTLIER) cc_final: 0.1373 (m170) REVERT: L 14 MET cc_start: 0.0309 (ppp) cc_final: -0.0036 (ppp) REVERT: H 75 MET cc_start: 0.2853 (mmt) cc_final: 0.1162 (ppp) outliers start: 89 outliers final: 65 residues processed: 279 average time/residue: 0.6492 time to fit residues: 286.5566 Evaluate side-chains 269 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 470 PHE Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 723 CYS Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 778 SER Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 33 PHE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 293 optimal weight: 0.0020 chunk 183 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.830 24678 Z= 0.792 Angle : 0.745 30.683 33339 Z= 0.396 Chirality : 0.047 0.181 3774 Planarity : 0.006 0.081 4348 Dihedral : 5.369 67.984 3378 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.58 % Favored : 90.00 % Rotamer: Outliers : 4.11 % Allowed : 22.77 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.15), residues: 3059 helix: -0.32 (0.17), residues: 959 sheet: 0.01 (0.29), residues: 330 loop : -2.19 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 199 HIS 0.010 0.002 HIS D 419 PHE 0.028 0.003 PHE C 40 TYR 0.037 0.003 TYR D 70 ARG 0.017 0.001 ARG D1079 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 215 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6703 (mm) REVERT: B 169 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7315 (mt) REVERT: C 31 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.4450 (pm20) REVERT: C 40 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5186 (t80) REVERT: C 131 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: C 274 LYS cc_start: 0.6622 (mmmt) cc_final: 0.5935 (mmmt) REVERT: C 403 HIS cc_start: 0.6520 (OUTLIER) cc_final: 0.5864 (t-90) REVERT: C 660 THR cc_start: 0.5313 (OUTLIER) cc_final: 0.4979 (p) REVERT: C 759 VAL cc_start: 0.5239 (OUTLIER) cc_final: 0.4722 (m) REVERT: C 889 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4760 (p0) REVERT: C 907 GLN cc_start: 0.3614 (pt0) cc_final: 0.3080 (pp30) REVERT: C 946 TYR cc_start: 0.5131 (p90) cc_final: 0.4059 (p90) REVERT: C 976 MET cc_start: 0.4974 (mmm) cc_final: 0.4152 (mmt) REVERT: C 1015 THR cc_start: 0.5558 (OUTLIER) cc_final: 0.5040 (t) REVERT: C 1074 ARG cc_start: 0.5713 (mtm-85) cc_final: 0.4465 (ttt90) REVERT: D 12 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5514 (tt) REVERT: D 470 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5858 (mtp180) REVERT: D 539 VAL cc_start: 0.3961 (p) cc_final: 0.3564 (p) REVERT: D 843 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6125 (mm) REVERT: F 44 HIS cc_start: 0.2739 (OUTLIER) cc_final: 0.1306 (m90) REVERT: L 14 MET cc_start: 0.0726 (ppp) cc_final: 0.0289 (ppp) REVERT: H 75 MET cc_start: 0.2914 (mmt) cc_final: 0.1543 (ppp) outliers start: 109 outliers final: 78 residues processed: 306 average time/residue: 0.6386 time to fit residues: 312.6709 Evaluate side-chains 298 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 206 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 759 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 778 SER Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 892 CYS Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 0.3980 chunk 199 optimal weight: 0.1980 chunk 144 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4987 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.825 24678 Z= 0.712 Angle : 0.581 30.758 33339 Z= 0.303 Chirality : 0.042 0.159 3774 Planarity : 0.004 0.060 4348 Dihedral : 4.835 66.040 3378 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.67 % Favored : 93.10 % Rotamer: Outliers : 3.05 % Allowed : 23.48 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 3059 helix: 0.20 (0.17), residues: 958 sheet: 0.14 (0.29), residues: 324 loop : -1.99 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.004 0.001 HIS B 220 PHE 0.012 0.001 PHE C1128 TYR 0.037 0.001 TYR D 70 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 200 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7268 (mt) REVERT: C 31 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.4177 (pm20) REVERT: C 274 LYS cc_start: 0.6635 (mmmt) cc_final: 0.5993 (mmmt) REVERT: C 403 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5606 (t-90) REVERT: C 660 THR cc_start: 0.4968 (p) cc_final: 0.4668 (p) REVERT: C 696 GLU cc_start: 0.4787 (mm-30) cc_final: 0.4560 (mm-30) REVERT: C 907 GLN cc_start: 0.3331 (pt0) cc_final: 0.2869 (pp30) REVERT: C 1015 THR cc_start: 0.5271 (OUTLIER) cc_final: 0.4838 (t) REVERT: D 12 ILE cc_start: 0.5686 (OUTLIER) cc_final: 0.5471 (tt) REVERT: D 539 VAL cc_start: 0.3831 (p) cc_final: 0.3442 (p) REVERT: D 843 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5806 (mm) REVERT: F 44 HIS cc_start: 0.2483 (OUTLIER) cc_final: 0.1107 (m90) REVERT: L 14 MET cc_start: 0.0534 (ppp) cc_final: 0.0159 (ppp) REVERT: H 75 MET cc_start: 0.2916 (mmt) cc_final: 0.1356 (ppp) outliers start: 81 outliers final: 66 residues processed: 269 average time/residue: 0.6451 time to fit residues: 275.5577 Evaluate side-chains 271 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 847 PHE Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 33 PHE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 256 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5024 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.825 24678 Z= 0.722 Angle : 0.594 30.599 33339 Z= 0.309 Chirality : 0.042 0.156 3774 Planarity : 0.004 0.059 4348 Dihedral : 4.803 65.095 3378 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.98 % Favored : 91.79 % Rotamer: Outliers : 3.09 % Allowed : 23.52 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 3059 helix: 0.23 (0.17), residues: 964 sheet: 0.08 (0.29), residues: 329 loop : -2.00 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.004 0.001 HIS D 419 PHE 0.014 0.001 PHE C 40 TYR 0.037 0.002 TYR D 70 ARG 0.004 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 206 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7211 (mt) REVERT: C 31 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.4155 (pm20) REVERT: C 274 LYS cc_start: 0.6607 (mmmt) cc_final: 0.5996 (mmmt) REVERT: C 285 LEU cc_start: 0.4578 (mm) cc_final: 0.3668 (tt) REVERT: C 403 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.5752 (t-90) REVERT: C 660 THR cc_start: 0.5109 (OUTLIER) cc_final: 0.4808 (p) REVERT: C 683 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: C 907 GLN cc_start: 0.3339 (pt0) cc_final: 0.2881 (pp30) REVERT: C 1015 THR cc_start: 0.5300 (OUTLIER) cc_final: 0.4858 (t) REVERT: D 19 LYS cc_start: 0.6983 (ptpt) cc_final: 0.6237 (mmtm) REVERT: D 539 VAL cc_start: 0.3782 (p) cc_final: 0.3373 (p) REVERT: D 843 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5823 (mm) REVERT: F 44 HIS cc_start: 0.2761 (OUTLIER) cc_final: 0.1394 (m90) REVERT: L 14 MET cc_start: 0.0593 (ppp) cc_final: 0.0211 (ppp) REVERT: H 75 MET cc_start: 0.2586 (mmt) cc_final: 0.1463 (ppp) outliers start: 82 outliers final: 68 residues processed: 275 average time/residue: 0.6106 time to fit residues: 270.1349 Evaluate side-chains 278 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 202 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 778 SER Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 176 HIS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 892 CYS Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 33 PHE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 241 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 186 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.824 24678 Z= 0.709 Angle : 0.558 30.699 33339 Z= 0.288 Chirality : 0.041 0.157 3774 Planarity : 0.004 0.058 4348 Dihedral : 4.588 62.251 3378 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.02 % Favored : 93.76 % Rotamer: Outliers : 2.64 % Allowed : 23.97 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3059 helix: 0.45 (0.17), residues: 966 sheet: 0.21 (0.29), residues: 317 loop : -1.91 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.003 0.001 HIS C 507 PHE 0.012 0.001 PHE D1099 TYR 0.037 0.001 TYR D 70 ARG 0.010 0.000 ARG C 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.3956 (pm20) REVERT: C 274 LYS cc_start: 0.6651 (mmmt) cc_final: 0.6021 (mmmt) REVERT: C 285 LEU cc_start: 0.4574 (mm) cc_final: 0.3668 (tt) REVERT: C 403 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5578 (t-90) REVERT: C 660 THR cc_start: 0.4923 (p) cc_final: 0.4629 (p) REVERT: C 907 GLN cc_start: 0.3310 (pt0) cc_final: 0.2870 (pp30) REVERT: D 19 LYS cc_start: 0.6965 (ptpt) cc_final: 0.6237 (mmtm) REVERT: D 539 VAL cc_start: 0.3901 (p) cc_final: 0.3487 (p) REVERT: D 546 ASN cc_start: 0.3212 (OUTLIER) cc_final: 0.2834 (m-40) REVERT: D 843 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5640 (mm) REVERT: F 44 HIS cc_start: 0.2800 (OUTLIER) cc_final: 0.1857 (m170) REVERT: L 14 MET cc_start: 0.0507 (ppp) cc_final: 0.0159 (ppp) REVERT: H 75 MET cc_start: 0.2582 (mmt) cc_final: 0.1470 (ppp) outliers start: 70 outliers final: 60 residues processed: 264 average time/residue: 0.6276 time to fit residues: 266.8332 Evaluate side-chains 262 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 510 HIS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1043 MET Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 631 PHE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 847 PHE Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1070 MET Chi-restraints excluded: chain D residue 1138 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 241 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5471 r_free = 0.5471 target = 0.304477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.261157 restraints weight = 87763.697| |-----------------------------------------------------------------------------| r_work (start): 0.5123 rms_B_bonded: 3.27 r_work: 0.4969 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4845 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5254 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.826 24678 Z= 0.729 Angle : 0.605 30.652 33339 Z= 0.315 Chirality : 0.042 0.155 3774 Planarity : 0.004 0.057 4348 Dihedral : 4.769 63.989 3378 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.17 % Favored : 91.60 % Rotamer: Outliers : 2.71 % Allowed : 24.01 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 3059 helix: 0.28 (0.17), residues: 965 sheet: 0.09 (0.29), residues: 322 loop : -1.98 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 199 HIS 0.005 0.001 HIS D 419 PHE 0.021 0.002 PHE C 40 TYR 0.037 0.002 TYR D 70 ARG 0.009 0.000 ARG C 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7260.61 seconds wall clock time: 126 minutes 34.27 seconds (7594.27 seconds total)