Starting phenix.real_space_refine on Wed Feb 21 01:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kin_22888/02_2024/7kin_22888.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kin_22888/02_2024/7kin_22888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kin_22888/02_2024/7kin_22888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kin_22888/02_2024/7kin_22888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kin_22888/02_2024/7kin_22888.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kin_22888/02_2024/7kin_22888.pdb" } resolution = 2.74 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= 0.004 sd= 0.119 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18088 2.51 5 N 5245 2.21 5 O 5841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 12": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C GLU 645": "OE1" <-> "OE2" Residue "C TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C GLU 786": "OE1" <-> "OE2" Residue "C ARG 787": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ASP 903": "OD1" <-> "OD2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ASP 947": "OD1" <-> "OD2" Residue "C PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D GLU 665": "OE1" <-> "OE2" Residue "D GLU 702": "OE1" <-> "OE2" Residue "D TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D GLU 750": "OE1" <-> "OE2" Residue "D GLU 772": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ASP 883": "OD1" <-> "OD2" Residue "D GLU 939": "OE1" <-> "OE2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D ASP 950": "OD1" <-> "OD2" Residue "D GLU 993": "OE1" <-> "OE2" Residue "D ARG 1041": "NH1" <-> "NH2" Residue "D ARG 1054": "NH1" <-> "NH2" Residue "D TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1140": "OE1" <-> "OE2" Residue "D GLU 1250": "OE1" <-> "OE2" Residue "D GLU 1277": "OE1" <-> "OE2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 35": "OD1" <-> "OD2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ASP 110": "OD1" <-> "OD2" Residue "M GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29379 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8606 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9914 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2510 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 308} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 870 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "O" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1096 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Chain: "P" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1009 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19155 SG CYS D 891 113.862 106.506 104.585 1.00 82.59 S ATOM 19722 SG CYS D 968 110.008 106.339 103.400 1.00 77.13 S ATOM 19764 SG CYS D 975 111.101 104.370 106.584 1.00 69.45 S ATOM 19782 SG CYS D 978 110.844 107.992 106.799 1.00 72.19 S ATOM 12593 SG CYS D 60 80.152 59.702 68.066 1.00102.84 S ATOM 12611 SG CYS D 62 78.677 59.399 64.784 1.00103.70 S ATOM 12720 SG CYS D 75 82.315 59.400 64.364 1.00107.31 S ATOM 12746 SG CYS D 78 80.340 62.643 64.995 1.00103.78 S Time building chain proxies: 15.48, per 1000 atoms: 0.53 Number of scatterers: 29379 At special positions: 0 Unit cell: (134.2, 162.8, 191.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 103 15.00 Mg 1 11.99 O 5841 8.00 N 5245 7.00 C 18088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.74 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 12 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6466 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 44 sheets defined 41.8% alpha, 14.7% beta 45 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 10.47 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.211A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.597A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.637A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.419A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.310A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.753A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.947A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.989A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 4.803A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.662A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.645A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.821A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1041 removed outlier: 3.566A pdb=" N LYS C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1090 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.362A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.812A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.921A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.887A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 186 removed outlier: 3.636A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.775A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.319A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.613A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.933A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.884A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.370A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.522A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.741A pdb=" N LEU D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.840A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.558A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.669A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.049A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.800A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1035 removed outlier: 3.526A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D1033 " --> pdb=" O PRO D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1125 removed outlier: 3.589A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1144 removed outlier: 3.600A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D1144 " --> pdb=" O GLU D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1153 Processing helix chain 'D' and resid 1154 through 1160 removed outlier: 3.820A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1187 Processing helix chain 'D' and resid 1211 through 1216 removed outlier: 3.548A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1237 removed outlier: 3.622A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.594A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.824A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.570A pdb=" N TRP F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.744A pdb=" N LYS F 339 " --> pdb=" O ASP F 336 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 340 " --> pdb=" O TYR F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 340' Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.823A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 408 through 417 Processing helix chain 'F' and resid 448 through 466 removed outlier: 3.629A pdb=" N THR F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.541A pdb=" N VAL F 475 " --> pdb=" O GLU F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'F' and resid 523 through 527 removed outlier: 3.639A pdb=" N LEU F 527 " --> pdb=" O ARG F 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 97 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 148 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.759A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.534A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.902A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.731A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.396A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.553A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.553A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU M 18 " --> pdb=" O LYS M 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.410A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.804A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 191 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.018A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.591A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.871A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.980A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C1026 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.613A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.714A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.691A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.749A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.492A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.606A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 138 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 328 through 329 Processing sheet with id=AD8, first strand: chain 'D' and resid 425 through 432 removed outlier: 7.414A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 632 through 637 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.808A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 6.924A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1077 Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.588A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'F' and resid 439 through 441 removed outlier: 3.610A pdb=" N GLY J 8 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 39 through 45 1211 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 14.31 Time building geometry restraints manager: 12.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4952 1.31 - 1.43: 7747 1.43 - 1.56: 17000 1.56 - 1.68: 205 1.68 - 1.81: 175 Bond restraints: 30079 Sorted by residual: bond pdb=" C GLY D 442 " pdb=" N LEU D 443 " ideal model delta sigma weight residual 1.332 1.241 0.092 1.44e-02 4.82e+03 4.04e+01 bond pdb=" C ASP C 733 " pdb=" O ASP C 733 " ideal model delta sigma weight residual 1.238 1.179 0.058 1.83e-02 2.99e+03 1.02e+01 bond pdb=" CB THR D1234 " pdb=" CG2 THR D1234 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" CB THR D 590 " pdb=" CG2 THR D 590 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.83e+00 bond pdb=" CB MET D 559 " pdb=" CG MET D 559 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.67e+00 ... (remaining 30074 not shown) Histogram of bond angle deviations from ideal: 95.25 - 103.98: 778 103.98 - 112.70: 16130 112.70 - 121.43: 16842 121.43 - 130.15: 7262 130.15 - 138.88: 158 Bond angle restraints: 41170 Sorted by residual: angle pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta sigma weight residual 121.54 135.25 -13.71 1.91e+00 2.74e-01 5.15e+01 angle pdb=" C ASP M 147 " pdb=" N ALA M 148 " pdb=" CA ALA M 148 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA TYR E 56 " pdb=" CB TYR E 56 " pdb=" CG TYR E 56 " ideal model delta sigma weight residual 113.90 122.08 -8.18 1.80e+00 3.09e-01 2.07e+01 angle pdb=" CA GLU C 962 " pdb=" CB GLU C 962 " pdb=" CG GLU C 962 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C GLU F 268 " pdb=" N ARG F 269 " pdb=" CA ARG F 269 " ideal model delta sigma weight residual 122.46 128.53 -6.07 1.41e+00 5.03e-01 1.86e+01 ... (remaining 41165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 17176 35.30 - 70.60: 916 70.60 - 105.91: 32 105.91 - 141.21: 0 141.21 - 176.51: 3 Dihedral angle restraints: 18127 sinusoidal: 8076 harmonic: 10051 Sorted by residual: dihedral pdb=" CA GLU C 962 " pdb=" C GLU C 962 " pdb=" N LEU C 963 " pdb=" CA LEU C 963 " ideal model delta harmonic sigma weight residual 180.00 142.06 37.94 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA PRO C 774 " pdb=" C PRO C 774 " pdb=" N ASN C 775 " pdb=" CA ASN C 775 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA SER C1093 " pdb=" C SER C1093 " pdb=" N ASP C1094 " pdb=" CA ASP C1094 " ideal model delta harmonic sigma weight residual -180.00 -147.89 -32.11 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 18124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3262 0.067 - 0.134: 1181 0.134 - 0.201: 204 0.201 - 0.268: 34 0.268 - 0.335: 9 Chirality restraints: 4690 Sorted by residual: chirality pdb=" CB VAL C1037 " pdb=" CA VAL C1037 " pdb=" CG1 VAL C1037 " pdb=" CG2 VAL C1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE C 702 " pdb=" CA ILE C 702 " pdb=" CG1 ILE C 702 " pdb=" CG2 ILE C 702 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB ILE D 320 " pdb=" CA ILE D 320 " pdb=" CG1 ILE D 320 " pdb=" CG2 ILE D 320 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 4687 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 579 " 0.033 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU D 579 " -0.111 2.00e-02 2.50e+03 pdb=" O LEU D 579 " 0.041 2.00e-02 2.50e+03 pdb=" N ASP D 580 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 148 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ALA M 148 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA M 148 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS M 149 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 444 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 445 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " -0.045 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 349 2.62 - 3.19: 23199 3.19 - 3.76: 44870 3.76 - 4.33: 61351 4.33 - 4.90: 104782 Nonbonded interactions: 234551 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.047 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.112 2.170 nonbonded pdb=" O SER D 338 " pdb=" OG SER D 338 " model vdw 2.173 2.440 nonbonded pdb=" OE2 GLU C 146 " pdb=" OH TYR M 11 " model vdw 2.237 2.440 nonbonded pdb=" OE2 GLU D 49 " pdb=" OG1 THR D 55 " model vdw 2.241 2.440 ... (remaining 234546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } 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=0.50 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: 1.830 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.790 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 90.780 Find NCS groups from input model: 1.180 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.016 0.138 30079 Z= 1.034 Angle : 1.049 18.167 41170 Z= 0.581 Chirality : 0.069 0.335 4690 Planarity : 0.009 0.083 5057 Dihedral : 18.369 176.509 11661 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 7.82 % Allowed : 11.61 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 3489 helix: -1.33 (0.12), residues: 1388 sheet: -1.30 (0.24), residues: 427 loop : -2.03 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 944 HIS 0.018 0.002 HIS C1042 PHE 0.033 0.004 PHE C 906 TYR 0.030 0.004 TYR D 586 ARG 0.008 0.001 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 303 time to evaluate : 3.074 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (ttmm) REVERT: A 91 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: A 224 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6570 (mm-30) REVERT: B 5 GLN cc_start: 0.7220 (tt0) cc_final: 0.6881 (tt0) REVERT: B 20 GLN cc_start: 0.8604 (tt0) cc_final: 0.8317 (tt0) REVERT: B 34 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 126 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7534 (t0) REVERT: C 190 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 220 ASP cc_start: 0.7973 (t0) cc_final: 0.7636 (t0) REVERT: C 298 ASN cc_start: 0.8112 (m110) cc_final: 0.7500 (m110) REVERT: C 303 GLU cc_start: 0.7695 (mp0) cc_final: 0.7363 (mp0) REVERT: C 305 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7796 (mtm180) REVERT: C 471 GLU cc_start: 0.8116 (tp30) cc_final: 0.7891 (tp30) REVERT: C 551 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7749 (p0) REVERT: C 584 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7938 (ptp-170) REVERT: C 672 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.7489 (mmp) REVERT: C 685 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8298 (m-40) REVERT: C 778 ASP cc_start: 0.8172 (t70) cc_final: 0.7754 (t0) REVERT: C 947 ASP cc_start: 0.7882 (p0) cc_final: 0.7296 (p0) REVERT: D 123 LYS cc_start: 0.7887 (mptp) cc_final: 0.7514 (mmtm) REVERT: D 138 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (p) REVERT: D 415 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7927 (tp-100) REVERT: D 480 ARG cc_start: 0.7855 (mpt90) cc_final: 0.7647 (mpt90) REVERT: D 581 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8826 (mtp) REVERT: D 598 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: D 688 MET cc_start: 0.8796 (mmt) cc_final: 0.8548 (mmt) REVERT: D 950 ASP cc_start: 0.8329 (m-30) cc_final: 0.7980 (m-30) REVERT: D 972 THR cc_start: 0.8355 (p) cc_final: 0.8117 (t) REVERT: D 1041 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7810 (ttm-80) REVERT: D 1115 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7223 (p) REVERT: F 468 SER cc_start: 0.5626 (OUTLIER) cc_final: 0.5286 (p) REVERT: J 7 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7546 (ttm110) outliers start: 229 outliers final: 118 residues processed: 486 average time/residue: 1.2500 time to fit residues: 725.5959 Evaluate side-chains 404 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 271 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 909 ASP Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.6980 chunk 269 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 279 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN C 415 GLN C 841 HIS C1042 HIS E 69 ASN E 70 GLN F 485 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30079 Z= 0.195 Angle : 0.561 13.327 41170 Z= 0.302 Chirality : 0.042 0.165 4690 Planarity : 0.006 0.074 5057 Dihedral : 17.502 179.825 5174 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.44 % Allowed : 15.98 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3489 helix: 0.33 (0.14), residues: 1376 sheet: -0.80 (0.26), residues: 391 loop : -1.60 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 70 HIS 0.003 0.001 HIS D 767 PHE 0.012 0.001 PHE C 906 TYR 0.011 0.001 TYR C1079 ARG 0.007 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 287 time to evaluate : 3.596 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7774 (tppp) REVERT: A 133 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8168 (ttmm) REVERT: A 224 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6309 (mm-30) REVERT: B 5 GLN cc_start: 0.7047 (tt0) cc_final: 0.6828 (tt0) REVERT: C 62 GLU cc_start: 0.7305 (pt0) cc_final: 0.7080 (mt-10) REVERT: C 195 THR cc_start: 0.8746 (m) cc_final: 0.8508 (t) REVERT: C 298 ASN cc_start: 0.8055 (m110) cc_final: 0.7395 (m110) REVERT: C 303 GLU cc_start: 0.7494 (mp0) cc_final: 0.7193 (mp0) REVERT: C 305 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7856 (mtm180) REVERT: C 645 GLU cc_start: 0.7791 (pt0) cc_final: 0.7384 (pt0) REVERT: C 702 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7224 (pt) REVERT: C 903 ASP cc_start: 0.7840 (p0) cc_final: 0.7545 (p0) REVERT: C 947 ASP cc_start: 0.7808 (p0) cc_final: 0.7267 (p0) REVERT: D 70 PHE cc_start: 0.7482 (m-80) cc_final: 0.7199 (m-80) REVERT: D 852 ASN cc_start: 0.7266 (t0) cc_final: 0.7049 (t0) REVERT: E 105 GLU cc_start: 0.8235 (pt0) cc_final: 0.7861 (pt0) REVERT: F 263 MET cc_start: 0.7333 (tpp) cc_final: 0.7062 (tpp) REVERT: F 468 SER cc_start: 0.5136 (OUTLIER) cc_final: 0.4890 (p) REVERT: J 7 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7551 (ttm110) outliers start: 130 outliers final: 75 residues processed: 391 average time/residue: 1.3039 time to fit residues: 606.8201 Evaluate side-chains 356 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 278 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 909 ASP Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 349 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 0.0980 chunk 259 optimal weight: 0.8980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 HIS E 70 GLN M 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30079 Z= 0.368 Angle : 0.614 16.012 41170 Z= 0.323 Chirality : 0.045 0.174 4690 Planarity : 0.005 0.072 5057 Dihedral : 17.260 179.772 5066 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.71 % Allowed : 17.04 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3489 helix: 0.74 (0.14), residues: 1392 sheet: -0.71 (0.26), residues: 402 loop : -1.52 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 723 HIS 0.005 0.001 HIS D 689 PHE 0.016 0.002 PHE C 906 TYR 0.020 0.002 TYR D 586 ARG 0.009 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 285 time to evaluate : 3.289 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7474 (ttmt) REVERT: A 133 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8193 (ttmm) REVERT: A 188 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: A 224 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6113 (mm-30) REVERT: B 5 GLN cc_start: 0.6977 (tt0) cc_final: 0.6766 (tt0) REVERT: C 195 THR cc_start: 0.8857 (m) cc_final: 0.8614 (t) REVERT: C 298 ASN cc_start: 0.8023 (m110) cc_final: 0.7390 (m110) REVERT: C 303 GLU cc_start: 0.7518 (mp0) cc_final: 0.7240 (mp0) REVERT: C 305 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7906 (mtm180) REVERT: C 308 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6037 (pp) REVERT: C 527 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7517 (mt-10) REVERT: C 661 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7524 (ttp) REVERT: C 685 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7762 (m-40) REVERT: C 947 ASP cc_start: 0.7859 (p0) cc_final: 0.7308 (p0) REVERT: C 1101 LYS cc_start: 0.7837 (mttt) cc_final: 0.7626 (mtpt) REVERT: D 56 ARG cc_start: 0.7382 (mtp85) cc_final: 0.7023 (ptp-110) REVERT: D 70 PHE cc_start: 0.7520 (m-80) cc_final: 0.7273 (m-80) REVERT: E 105 GLU cc_start: 0.8184 (pt0) cc_final: 0.7844 (pt0) REVERT: J 7 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7502 (ttm110) outliers start: 138 outliers final: 89 residues processed: 389 average time/residue: 1.3430 time to fit residues: 619.3473 Evaluate side-chains 367 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 273 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 308 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN M 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30079 Z= 0.231 Angle : 0.545 15.015 41170 Z= 0.289 Chirality : 0.042 0.161 4690 Planarity : 0.005 0.073 5057 Dihedral : 16.933 179.124 5050 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.17 % Allowed : 17.96 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3489 helix: 1.15 (0.14), residues: 1395 sheet: -0.54 (0.27), residues: 373 loop : -1.38 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 723 HIS 0.003 0.001 HIS C 372 PHE 0.012 0.001 PHE C 906 TYR 0.013 0.001 TYR D 586 ARG 0.008 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 288 time to evaluate : 3.707 Fit side-chains REVERT: A 81 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7491 (ttmt) REVERT: A 133 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8190 (ttmm) REVERT: A 188 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: A 224 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6059 (mm-30) REVERT: B 5 GLN cc_start: 0.6955 (tt0) cc_final: 0.6725 (tt0) REVERT: C 126 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7445 (t0) REVERT: C 195 THR cc_start: 0.8864 (m) cc_final: 0.8601 (t) REVERT: C 298 ASN cc_start: 0.7960 (m110) cc_final: 0.7383 (m110) REVERT: C 302 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6527 (tttp) REVERT: C 305 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7975 (mtm180) REVERT: C 308 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5781 (pp) REVERT: C 527 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 661 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7573 (ttp) REVERT: C 667 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8109 (ptt-90) REVERT: C 903 ASP cc_start: 0.8062 (p0) cc_final: 0.7754 (p0) REVERT: C 947 ASP cc_start: 0.7800 (p0) cc_final: 0.7339 (p0) REVERT: D 56 ARG cc_start: 0.7362 (mtp85) cc_final: 0.7007 (ptp-110) REVERT: D 70 PHE cc_start: 0.7461 (m-80) cc_final: 0.7213 (m-80) REVERT: D 706 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: E 105 GLU cc_start: 0.8058 (pt0) cc_final: 0.7700 (pt0) REVERT: F 277 GLN cc_start: 0.7945 (tp40) cc_final: 0.7578 (mm110) REVERT: F 279 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7510 (ttp80) REVERT: F 315 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: F 468 SER cc_start: 0.4997 (OUTLIER) cc_final: 0.4795 (p) REVERT: J 7 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7446 (ttm110) outliers start: 122 outliers final: 72 residues processed: 379 average time/residue: 1.3322 time to fit residues: 599.0787 Evaluate side-chains 363 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 281 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 3.9990 chunk 195 optimal weight: 0.0000 chunk 4 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 237 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 175 optimal weight: 0.0870 chunk 308 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 GLN C 415 GLN ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS C1066 GLN D 693 GLN D 852 ASN D 854 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30079 Z= 0.153 Angle : 0.499 12.029 41170 Z= 0.266 Chirality : 0.040 0.162 4690 Planarity : 0.004 0.067 5057 Dihedral : 16.670 178.722 5032 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.83 % Allowed : 18.41 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3489 helix: 1.56 (0.14), residues: 1391 sheet: -0.44 (0.27), residues: 392 loop : -1.21 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.003 0.000 HIS M 13 PHE 0.010 0.001 PHE C 153 TYR 0.011 0.001 TYR C 731 ARG 0.009 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 312 time to evaluate : 3.125 Fit side-chains REVERT: A 131 LYS cc_start: 0.8734 (mttm) cc_final: 0.8469 (mttp) REVERT: A 133 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8189 (ttmm) REVERT: A 188 ASP cc_start: 0.7669 (m-30) cc_final: 0.7418 (m-30) REVERT: A 213 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7517 (ttmt) REVERT: A 224 GLU cc_start: 0.6447 (mm-30) cc_final: 0.6133 (mm-30) REVERT: B 5 GLN cc_start: 0.6873 (tt0) cc_final: 0.6620 (tt0) REVERT: B 52 THR cc_start: 0.8721 (m) cc_final: 0.8486 (p) REVERT: B 55 ARG cc_start: 0.7186 (mpt180) cc_final: 0.6870 (mpt90) REVERT: B 195 ASP cc_start: 0.7600 (t0) cc_final: 0.7279 (t0) REVERT: C 69 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.7054 (ttp-110) REVERT: C 195 THR cc_start: 0.8863 (m) cc_final: 0.8567 (t) REVERT: C 298 ASN cc_start: 0.7926 (m110) cc_final: 0.7424 (m110) REVERT: C 302 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6478 (tttp) REVERT: C 527 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7424 (tt0) REVERT: C 661 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7662 (ttp) REVERT: C 852 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8132 (t) REVERT: C 909 ASP cc_start: 0.7436 (t0) cc_final: 0.7079 (m-30) REVERT: C 947 ASP cc_start: 0.7802 (p0) cc_final: 0.7385 (p0) REVERT: D 155 MET cc_start: 0.7469 (tpp) cc_final: 0.7048 (tpt) REVERT: D 327 MET cc_start: 0.8538 (ttp) cc_final: 0.8239 (ttp) REVERT: D 950 ASP cc_start: 0.8311 (m-30) cc_final: 0.7896 (m-30) REVERT: E 105 GLU cc_start: 0.7986 (pt0) cc_final: 0.7624 (pt0) REVERT: F 221 LEU cc_start: 0.6267 (pp) cc_final: 0.5959 (pt) REVERT: F 266 LEU cc_start: 0.7391 (tp) cc_final: 0.7032 (tt) REVERT: F 277 GLN cc_start: 0.7965 (tp40) cc_final: 0.7645 (mm110) REVERT: F 279 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7469 (ttp80) REVERT: J 7 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7557 (ttm110) REVERT: J 92 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8220 (pm20) outliers start: 112 outliers final: 58 residues processed: 395 average time/residue: 1.3225 time to fit residues: 620.8236 Evaluate side-chains 360 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 297 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 0.7980 chunk 309 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 84 optimal weight: 0.0670 chunk 344 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30079 Z= 0.202 Angle : 0.525 13.769 41170 Z= 0.277 Chirality : 0.041 0.179 4690 Planarity : 0.005 0.065 5057 Dihedral : 16.649 178.841 5013 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.13 % Allowed : 18.72 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3489 helix: 1.65 (0.14), residues: 1387 sheet: -0.35 (0.27), residues: 390 loop : -1.16 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 723 HIS 0.003 0.001 HIS D 689 PHE 0.011 0.001 PHE D1061 TYR 0.014 0.001 TYR D 586 ARG 0.011 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 306 time to evaluate : 3.595 Fit side-chains REVERT: A 81 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7480 (ttmt) REVERT: A 133 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8213 (ttmm) REVERT: A 188 ASP cc_start: 0.7666 (m-30) cc_final: 0.7423 (m-30) REVERT: A 213 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7507 (ttmt) REVERT: A 224 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6349 (mm-30) REVERT: B 5 GLN cc_start: 0.6923 (tt0) cc_final: 0.6664 (tt0) REVERT: B 52 THR cc_start: 0.8771 (m) cc_final: 0.8474 (p) REVERT: B 55 ARG cc_start: 0.7200 (mpt180) cc_final: 0.6874 (mpt90) REVERT: B 195 ASP cc_start: 0.7584 (t0) cc_final: 0.7264 (t0) REVERT: C 142 ASN cc_start: 0.7341 (m110) cc_final: 0.6656 (m-40) REVERT: C 298 ASN cc_start: 0.7924 (m110) cc_final: 0.7492 (m-40) REVERT: C 302 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6428 (tttp) REVERT: C 435 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: C 527 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7423 (tt0) REVERT: C 661 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7646 (ttp) REVERT: C 852 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8126 (t) REVERT: C 909 ASP cc_start: 0.7412 (t0) cc_final: 0.7062 (m-30) REVERT: C 947 ASP cc_start: 0.7799 (p0) cc_final: 0.7383 (p0) REVERT: D 155 MET cc_start: 0.7391 (tpp) cc_final: 0.7144 (tpt) REVERT: D 491 ILE cc_start: 0.7873 (tt) cc_final: 0.7411 (pp) REVERT: D 950 ASP cc_start: 0.8322 (m-30) cc_final: 0.7909 (m-30) REVERT: D 1005 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8067 (tt0) REVERT: E 105 GLU cc_start: 0.7986 (pt0) cc_final: 0.7641 (pt0) REVERT: F 221 LEU cc_start: 0.6277 (pp) cc_final: 0.5965 (pt) REVERT: F 277 GLN cc_start: 0.8027 (tp40) cc_final: 0.7801 (mp10) REVERT: F 279 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7836 (ttp-110) REVERT: J 92 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: M 13 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7157 (t70) REVERT: M 151 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7653 (mm-30) outliers start: 121 outliers final: 75 residues processed: 398 average time/residue: 1.3274 time to fit residues: 629.2534 Evaluate side-chains 378 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 294 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 151 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 192 optimal weight: 0.3980 chunk 343 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS D 369 ASN D 854 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30079 Z= 0.240 Angle : 0.542 14.440 41170 Z= 0.284 Chirality : 0.042 0.200 4690 Planarity : 0.005 0.064 5057 Dihedral : 16.632 178.721 5012 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.30 % Allowed : 18.85 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3489 helix: 1.65 (0.14), residues: 1386 sheet: -0.32 (0.27), residues: 388 loop : -1.14 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 723 HIS 0.004 0.001 HIS C1042 PHE 0.013 0.001 PHE C 906 TYR 0.015 0.001 TYR D 586 ARG 0.011 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 296 time to evaluate : 3.210 Fit side-chains REVERT: A 81 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7435 (ttmt) REVERT: A 133 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8217 (ttmm) REVERT: A 188 ASP cc_start: 0.7665 (m-30) cc_final: 0.7418 (m-30) REVERT: A 224 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6347 (mm-30) REVERT: B 5 GLN cc_start: 0.6937 (tt0) cc_final: 0.6672 (tt0) REVERT: B 55 ARG cc_start: 0.7205 (mpt180) cc_final: 0.6911 (mpt90) REVERT: B 195 ASP cc_start: 0.7610 (t0) cc_final: 0.7312 (t0) REVERT: C 142 ASN cc_start: 0.7363 (m110) cc_final: 0.6717 (m110) REVERT: C 298 ASN cc_start: 0.7930 (m110) cc_final: 0.7470 (m-40) REVERT: C 302 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6349 (tttp) REVERT: C 435 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: C 527 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7420 (tt0) REVERT: C 661 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7662 (ttp) REVERT: C 852 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8115 (t) REVERT: C 909 ASP cc_start: 0.7446 (t0) cc_final: 0.7082 (m-30) REVERT: C 947 ASP cc_start: 0.7816 (p0) cc_final: 0.7388 (p0) REVERT: D 123 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6861 (mmtm) REVERT: D 155 MET cc_start: 0.7455 (tpp) cc_final: 0.7194 (tpt) REVERT: D 488 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: D 950 ASP cc_start: 0.8321 (m-30) cc_final: 0.7863 (m-30) REVERT: E 105 GLU cc_start: 0.8011 (pt0) cc_final: 0.7662 (pt0) REVERT: F 221 LEU cc_start: 0.6297 (pp) cc_final: 0.5983 (pt) REVERT: J 7 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7365 (ttm110) REVERT: J 92 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: M 13 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7181 (t70) REVERT: M 151 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7671 (mm-30) outliers start: 126 outliers final: 83 residues processed: 392 average time/residue: 1.3829 time to fit residues: 641.4552 Evaluate side-chains 376 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 284 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 151 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS D 369 ASN D 854 HIS E 70 GLN F 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30079 Z= 0.218 Angle : 0.540 14.446 41170 Z= 0.282 Chirality : 0.042 0.206 4690 Planarity : 0.005 0.063 5057 Dihedral : 16.579 178.659 5012 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 19.06 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3489 helix: 1.72 (0.14), residues: 1387 sheet: -0.27 (0.27), residues: 388 loop : -1.10 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 723 HIS 0.003 0.001 HIS C1042 PHE 0.011 0.001 PHE D1061 TYR 0.014 0.001 TYR D 586 ARG 0.012 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 294 time to evaluate : 3.555 Fit side-chains REVERT: A 81 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7411 (ttmt) REVERT: A 133 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8194 (ttmm) REVERT: A 188 ASP cc_start: 0.7645 (m-30) cc_final: 0.7385 (m-30) REVERT: A 213 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7497 (ttmt) REVERT: A 224 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6332 (mm-30) REVERT: B 5 GLN cc_start: 0.6934 (tt0) cc_final: 0.6671 (tt0) REVERT: B 55 ARG cc_start: 0.7148 (mpt180) cc_final: 0.6868 (mpt90) REVERT: B 195 ASP cc_start: 0.7636 (t0) cc_final: 0.7311 (t0) REVERT: C 142 ASN cc_start: 0.7443 (m110) cc_final: 0.6891 (m110) REVERT: C 203 LYS cc_start: 0.7449 (mtmm) cc_final: 0.7083 (mtpt) REVERT: C 298 ASN cc_start: 0.7917 (m110) cc_final: 0.7474 (m-40) REVERT: C 302 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6512 (tttp) REVERT: C 435 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: C 527 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7424 (tt0) REVERT: C 661 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7676 (ttp) REVERT: C 852 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8115 (t) REVERT: C 909 ASP cc_start: 0.7421 (t0) cc_final: 0.7059 (m-30) REVERT: C 947 ASP cc_start: 0.7716 (p0) cc_final: 0.7363 (p0) REVERT: D 123 LYS cc_start: 0.7245 (mmtm) cc_final: 0.6850 (mmtm) REVERT: D 155 MET cc_start: 0.7559 (tpp) cc_final: 0.7276 (tpt) REVERT: D 238 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6246 (tp30) REVERT: D 242 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7807 (tpp80) REVERT: D 488 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6531 (mt-10) REVERT: D 950 ASP cc_start: 0.8323 (m-30) cc_final: 0.7881 (m-30) REVERT: E 105 GLU cc_start: 0.8013 (pt0) cc_final: 0.7678 (pt0) REVERT: F 217 LYS cc_start: 0.7188 (mmtt) cc_final: 0.6644 (mmtp) REVERT: F 221 LEU cc_start: 0.6280 (pp) cc_final: 0.5969 (pt) REVERT: J 7 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7376 (ttm110) REVERT: J 92 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: M 13 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.7157 (t70) REVERT: M 151 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7678 (mm-30) outliers start: 119 outliers final: 86 residues processed: 386 average time/residue: 1.3346 time to fit residues: 614.1226 Evaluate side-chains 382 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 286 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 151 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.7980 chunk 328 optimal weight: 0.0060 chunk 299 optimal weight: 0.9990 chunk 319 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 288 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS D 854 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30079 Z= 0.161 Angle : 0.511 12.945 41170 Z= 0.269 Chirality : 0.041 0.194 4690 Planarity : 0.004 0.064 5057 Dihedral : 16.443 178.669 5012 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.55 % Allowed : 19.74 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3489 helix: 1.89 (0.14), residues: 1386 sheet: -0.19 (0.27), residues: 392 loop : -1.02 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 723 HIS 0.003 0.000 HIS D 854 PHE 0.011 0.001 PHE D1061 TYR 0.012 0.001 TYR C 731 ARG 0.012 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 301 time to evaluate : 3.428 Fit side-chains REVERT: A 133 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8171 (ttmm) REVERT: A 213 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7528 (ttmt) REVERT: A 224 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6143 (mm-30) REVERT: B 5 GLN cc_start: 0.6864 (tt0) cc_final: 0.6597 (tt0) REVERT: B 52 THR cc_start: 0.8746 (m) cc_final: 0.8508 (p) REVERT: B 55 ARG cc_start: 0.7074 (mpt180) cc_final: 0.6826 (mpt90) REVERT: B 195 ASP cc_start: 0.7591 (t0) cc_final: 0.7282 (t0) REVERT: C 142 ASN cc_start: 0.7475 (m110) cc_final: 0.6936 (m110) REVERT: C 203 LYS cc_start: 0.7435 (mtmm) cc_final: 0.7117 (mtpt) REVERT: C 225 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.7004 (ttm-80) REVERT: C 298 ASN cc_start: 0.7908 (m110) cc_final: 0.7333 (m-40) REVERT: C 527 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7449 (tt0) REVERT: C 661 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7705 (ttp) REVERT: C 909 ASP cc_start: 0.7312 (t0) cc_final: 0.6975 (m-30) REVERT: D 155 MET cc_start: 0.7547 (tpp) cc_final: 0.7279 (tpt) REVERT: D 238 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6711 (tp30) REVERT: D 488 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: D 725 THR cc_start: 0.8027 (t) cc_final: 0.7757 (t) REVERT: D 950 ASP cc_start: 0.8325 (m-30) cc_final: 0.7911 (m-30) REVERT: E 105 GLU cc_start: 0.7988 (pt0) cc_final: 0.7627 (pt0) REVERT: F 217 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6848 (mmtp) REVERT: F 245 GLU cc_start: 0.7956 (tp30) cc_final: 0.7665 (mt-10) REVERT: F 266 LEU cc_start: 0.7720 (tp) cc_final: 0.7339 (tt) REVERT: F 341 TYR cc_start: 0.9002 (m-80) cc_final: 0.8716 (m-80) REVERT: J 7 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7294 (ttm110) REVERT: J 92 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: M 13 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7140 (t70) REVERT: M 151 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7649 (mm-30) outliers start: 104 outliers final: 75 residues processed: 383 average time/residue: 1.3220 time to fit residues: 607.3243 Evaluate side-chains 371 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 290 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 704 ASP Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 415 GLN Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 1.9990 chunk 338 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 235 optimal weight: 0.0980 chunk 354 optimal weight: 10.0000 chunk 326 optimal weight: 0.0870 chunk 282 optimal weight: 0.0970 chunk 29 optimal weight: 0.2980 chunk 218 optimal weight: 0.8980 chunk 173 optimal weight: 50.0000 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN C 388 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS D 854 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 299 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30079 Z= 0.139 Angle : 0.498 13.196 41170 Z= 0.262 Chirality : 0.040 0.187 4690 Planarity : 0.004 0.065 5057 Dihedral : 16.330 178.842 5010 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.49 % Allowed : 20.90 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3489 helix: 2.00 (0.14), residues: 1395 sheet: -0.16 (0.27), residues: 399 loop : -0.87 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 723 HIS 0.003 0.000 HIS D 854 PHE 0.012 0.001 PHE D1061 TYR 0.012 0.001 TYR C 731 ARG 0.013 0.000 ARG D1085 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 327 time to evaluate : 3.209 Fit side-chains REVERT: A 62 GLU cc_start: 0.7881 (tt0) cc_final: 0.7576 (tt0) REVERT: A 133 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8145 (ttmm) REVERT: A 213 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7471 (ttmt) REVERT: A 224 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6111 (mm-30) REVERT: B 55 ARG cc_start: 0.7054 (mpt180) cc_final: 0.6846 (mpt90) REVERT: B 179 ASP cc_start: 0.7640 (m-30) cc_final: 0.7433 (m-30) REVERT: B 195 ASP cc_start: 0.7635 (t0) cc_final: 0.7353 (t0) REVERT: C 142 ASN cc_start: 0.7590 (m110) cc_final: 0.7035 (m110) REVERT: C 298 ASN cc_start: 0.7834 (m110) cc_final: 0.7284 (m-40) REVERT: C 527 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7503 (tt0) REVERT: C 661 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: C 909 ASP cc_start: 0.6940 (t0) cc_final: 0.6696 (m-30) REVERT: D 155 MET cc_start: 0.7451 (tpp) cc_final: 0.7195 (tpt) REVERT: D 238 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6249 (tp30) REVERT: D 242 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7842 (tpp80) REVERT: D 491 ILE cc_start: 0.7829 (tt) cc_final: 0.7391 (pp) REVERT: D 576 MET cc_start: 0.7965 (ttm) cc_final: 0.7730 (ttt) REVERT: D 725 THR cc_start: 0.7948 (t) cc_final: 0.7644 (t) REVERT: D 950 ASP cc_start: 0.8330 (m-30) cc_final: 0.7875 (m-30) REVERT: D 1115 SER cc_start: 0.7886 (m) cc_final: 0.7360 (p) REVERT: E 105 GLU cc_start: 0.7907 (pt0) cc_final: 0.7547 (pt0) REVERT: F 217 LYS cc_start: 0.7371 (mmtt) cc_final: 0.6909 (mmtp) REVERT: F 245 GLU cc_start: 0.7933 (tp30) cc_final: 0.7671 (mt-10) REVERT: F 266 LEU cc_start: 0.7683 (tp) cc_final: 0.7294 (tt) REVERT: J 7 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7343 (ttm110) REVERT: J 92 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: M 13 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7093 (t70) REVERT: M 59 ARG cc_start: 0.7271 (ttp80) cc_final: 0.6768 (ptt90) REVERT: M 151 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7649 (mm-30) outliers start: 73 outliers final: 50 residues processed: 388 average time/residue: 1.2903 time to fit residues: 597.4081 Evaluate side-chains 354 residues out of total 2961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 299 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.0010 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 282 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 36 ASN B 200 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 GLN J 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.095920 restraints weight = 35258.550| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.47 r_work: 0.2978 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30079 Z= 0.199 Angle : 0.536 13.487 41170 Z= 0.279 Chirality : 0.041 0.216 4690 Planarity : 0.004 0.064 5057 Dihedral : 16.350 178.799 4997 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.32 % Allowed : 21.48 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3489 helix: 1.95 (0.14), residues: 1390 sheet: -0.06 (0.27), residues: 398 loop : -0.89 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 723 HIS 0.003 0.001 HIS D 689 PHE 0.011 0.001 PHE D1061 TYR 0.014 0.001 TYR D 586 ARG 0.013 0.000 ARG D1085 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10914.02 seconds wall clock time: 194 minutes 1.97 seconds (11641.97 seconds total)