Starting phenix.real_space_refine on Mon Jun 16 04:25:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ipt_35643/06_2025/8ipt_35643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipt_35643/06_2025/8ipt_35643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ipt_35643/06_2025/8ipt_35643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipt_35643/06_2025/8ipt_35643.map" model { file = "/net/cci-nas-00/data/ceres_data/8ipt_35643/06_2025/8ipt_35643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipt_35643/06_2025/8ipt_35643.cif" } resolution = 3.5 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= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 11618 2.51 5 N 3198 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18178 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4594 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "D" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "E" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4594 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.13, per 1000 atoms: 0.56 Number of scatterers: 18178 At special positions: 0 Unit cell: (90.24, 106.56, 229.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3290 8.00 N 3198 7.00 C 11618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.06 Conformation dependent library (CDL) restraints added in 2.8 seconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 10 sheets defined 64.6% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 14 through 49 removed outlier: 3.570A pdb=" N GLY C 21 " --> pdb=" O MET C 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 60 through 104 removed outlier: 3.660A pdb=" N GLY C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 removed outlier: 4.215A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 138 through 156 Processing helix chain 'C' and resid 159 through 207 removed outlier: 3.716A pdb=" N ALA C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 4.614A pdb=" N ARG C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 219 through 266 removed outlier: 4.010A pdb=" N GLN C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.510A pdb=" N ALA C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.874A pdb=" N ALA C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 removed outlier: 3.931A pdb=" N VAL C 307 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 removed outlier: 3.688A pdb=" N LEU C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.523A pdb=" N ARG C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.691A pdb=" N VAL C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.942A pdb=" N LYS C 570 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 572 " --> pdb=" O GLN C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 566 through 572' Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.962A pdb=" N GLN A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 55 removed outlier: 3.820A pdb=" N ILE A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.515A pdb=" N ALA A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 110 removed outlier: 4.360A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.504A pdb=" N ILE A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 115' Processing helix chain 'A' and resid 118 through 132 removed outlier: 3.785A pdb=" N GLN A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.458A pdb=" N ALA A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.943A pdb=" N ALA A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.380A pdb=" N LEU A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.836A pdb=" N ARG A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.680A pdb=" N LEU A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 273 removed outlier: 3.595A pdb=" N ARG A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 328 removed outlier: 3.570A pdb=" N GLY A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Proline residue: A 298 - end of helix Proline residue: A 303 - end of helix removed outlier: 4.079A pdb=" N HIS A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.681A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.651A pdb=" N VAL A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.797A pdb=" N GLN A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.557A pdb=" N LEU A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 3.834A pdb=" N GLN A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 575 through 588 removed outlier: 3.516A pdb=" N ILE A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 3 No H-bonds generated for 'chain 'D' and resid 1 through 3' Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 14 through 49 removed outlier: 3.570A pdb=" N GLY D 21 " --> pdb=" O MET D 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 104 removed outlier: 3.660A pdb=" N GLY D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 4.215A pdb=" N LEU D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 136 Processing helix chain 'D' and resid 138 through 156 Processing helix chain 'D' and resid 159 through 207 removed outlier: 3.716A pdb=" N ALA D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.614A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 266 removed outlier: 4.010A pdb=" N GLN D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.510A pdb=" N ALA D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.874A pdb=" N ALA D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS D 303 " --> pdb=" O GLY D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.931A pdb=" N VAL D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.688A pdb=" N LEU D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.523A pdb=" N ARG D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.692A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 487 Processing helix chain 'D' and resid 506 through 521 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.941A pdb=" N LYS D 570 " --> pdb=" O TYR D 566 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 572 " --> pdb=" O GLN D 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 572' Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.962A pdb=" N GLN E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 55 removed outlier: 3.821A pdb=" N ILE E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 55 " --> pdb=" O HIS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 removed outlier: 3.515A pdb=" N ALA E 61 " --> pdb=" O PRO E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 61' Processing helix chain 'E' and resid 62 through 110 removed outlier: 4.361A pdb=" N PHE E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.503A pdb=" N ILE E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 115' Processing helix chain 'E' and resid 118 through 132 removed outlier: 3.785A pdb=" N GLN E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 Processing helix chain 'E' and resid 139 through 159 removed outlier: 4.459A pdb=" N ALA E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL E 148 " --> pdb=" O MET E 144 " (cutoff:3.500A) Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.943A pdb=" N ALA E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.380A pdb=" N LEU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 211 removed outlier: 3.835A pdb=" N ARG E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.680A pdb=" N LEU E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 273 removed outlier: 3.595A pdb=" N ARG E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 328 removed outlier: 3.570A pdb=" N GLY E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Proline residue: E 298 - end of helix Proline residue: E 303 - end of helix removed outlier: 4.079A pdb=" N HIS E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 313 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU E 324 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 412 through 416 removed outlier: 3.681A pdb=" N ASP E 415 " --> pdb=" O GLU E 412 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 412 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 423 through 425 No H-bonds generated for 'chain 'E' and resid 423 through 425' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.650A pdb=" N VAL E 443 " --> pdb=" O LEU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.796A pdb=" N GLN E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 removed outlier: 3.557A pdb=" N LEU E 471 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 500 removed outlier: 3.834A pdb=" N GLN E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 494 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 533 Processing helix chain 'E' and resid 566 through 571 Processing helix chain 'E' and resid 575 through 588 removed outlier: 3.516A pdb=" N ILE E 588 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.645A pdb=" N THR C 340 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 342 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL C 344 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN C 394 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 417 through 419 removed outlier: 3.655A pdb=" N LEU C 527 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 498 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 368 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE C 542 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA C 370 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL C 544 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 372 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 541 " --> pdb=" O GLU C 552 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU C 552 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE C 543 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 372 removed outlier: 5.646A pdb=" N LEU A 369 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.612A pdb=" N VAL A 380 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET A 556 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A 382 " --> pdb=" O MET A 556 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 563 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN A 557 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.591A pdb=" N LEU A 507 " --> pdb=" O LEU A 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 361 through 363 removed outlier: 3.645A pdb=" N THR D 340 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 342 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU D 396 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL D 344 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN D 394 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 417 through 419 removed outlier: 3.656A pdb=" N LEU D 527 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 498 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE D 369 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS D 368 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE D 542 " --> pdb=" O HIS D 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 370 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL D 544 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 372 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN D 541 " --> pdb=" O GLU D 552 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU D 552 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE D 543 " --> pdb=" O ILE D 550 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 372 removed outlier: 5.646A pdb=" N LEU E 369 " --> pdb=" O ASP E 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.611A pdb=" N VAL E 380 " --> pdb=" O TRP E 554 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET E 556 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL E 382 " --> pdb=" O MET E 556 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 563 " --> pdb=" O VAL E 555 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN E 557 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE E 561 " --> pdb=" O GLN E 557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 507 through 509 removed outlier: 6.592A pdb=" N LEU E 507 " --> pdb=" O LEU E 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 960 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5322 1.34 - 1.45: 2719 1.45 - 1.57: 10367 1.57 - 1.69: 20 1.69 - 1.81: 114 Bond restraints: 18542 Sorted by residual: bond pdb=" N PHE E 159 " pdb=" CA PHE E 159 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.02e+01 bond pdb=" N ILE A 158 " pdb=" CA ILE A 158 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 bond pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.37e+00 bond pdb=" N ILE E 357 " pdb=" CA ILE E 357 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.06e+00 bond pdb=" N ILE E 158 " pdb=" CA ILE E 158 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.33e-02 5.65e+03 7.47e+00 ... (remaining 18537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 24704 2.00 - 3.99: 391 3.99 - 5.99: 100 5.99 - 7.99: 15 7.99 - 9.98: 6 Bond angle restraints: 25216 Sorted by residual: angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.96e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 129.90 9.97 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 130.25 9.62 1.00e+00 1.00e+00 9.26e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 130.26 9.61 1.00e+00 1.00e+00 9.23e+01 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 129.59 7.24 1.00e+00 1.00e+00 5.24e+01 ... (remaining 25211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9247 17.88 - 35.76: 1455 35.76 - 53.64: 339 53.64 - 71.52: 59 71.52 - 89.40: 36 Dihedral angle restraints: 11136 sinusoidal: 4474 harmonic: 6662 Sorted by residual: dihedral pdb=" CA ASN C 58 " pdb=" C ASN C 58 " pdb=" N TYR C 59 " pdb=" CA TYR C 59 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN D 58 " pdb=" C ASN D 58 " pdb=" N TYR D 59 " pdb=" CA TYR D 59 " ideal model delta harmonic sigma weight residual -180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N ASN C 58 " pdb=" CA ASN C 58 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2139 0.038 - 0.076: 613 0.076 - 0.114: 147 0.114 - 0.152: 23 0.152 - 0.190: 6 Chirality restraints: 2928 Sorted by residual: chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2925 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 273 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ASN D 273 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN D 273 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 274 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 273 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ASN C 273 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN C 273 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA C 274 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO E 151 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.025 5.00e-02 4.00e+02 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1371 2.74 - 3.28: 18002 3.28 - 3.82: 28524 3.82 - 4.36: 31212 4.36 - 4.90: 56484 Nonbonded interactions: 135593 Sorted by model distance: nonbonded pdb=" NE2 GLN C 553 " pdb=" CG2 THR C 555 " model vdw 2.200 3.540 nonbonded pdb=" NE2 GLN D 553 " pdb=" CG2 THR D 555 " model vdw 2.200 3.540 nonbonded pdb=" NH2 ARG A 99 " pdb=" OD1 ASP A 131 " model vdw 2.269 3.120 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD1 ASP E 131 " model vdw 2.269 3.120 nonbonded pdb=" CG2 THR C 555 " pdb=" OE1 GLU C 558 " model vdw 2.295 3.460 ... (remaining 135588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 42.220 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18542 Z= 0.181 Angle : 0.672 9.982 25216 Z= 0.383 Chirality : 0.039 0.190 2928 Planarity : 0.004 0.045 3206 Dihedral : 18.348 89.402 6840 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 0.32 % Allowed : 31.97 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.19), residues: 2314 helix: 1.91 (0.15), residues: 1294 sheet: -1.68 (0.50), residues: 108 loop : -2.93 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 550 HIS 0.004 0.001 HIS A 519 PHE 0.012 0.001 PHE C 145 TYR 0.012 0.001 TYR A 88 ARG 0.005 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.14672 ( 960) hydrogen bonds : angle 5.45333 ( 2844) covalent geometry : bond 0.00312 (18542) covalent geometry : angle 0.67189 (25216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8344 (mmm) cc_final: 0.8114 (mtp) REVERT: E 159 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8086 (t80) outliers start: 6 outliers final: 2 residues processed: 265 average time/residue: 0.3725 time to fit residues: 143.0438 Evaluate side-chains 153 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 416 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN A 394 ASN A 403 GLN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.129153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097520 restraints weight = 34691.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100338 restraints weight = 18076.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102259 restraints weight = 11586.605| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18542 Z= 0.157 Angle : 0.620 9.544 25216 Z= 0.318 Chirality : 0.040 0.203 2928 Planarity : 0.005 0.078 3206 Dihedral : 7.877 76.115 2672 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.08 % Favored : 90.84 % Rotamer: Outliers : 3.34 % Allowed : 29.80 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.19), residues: 2314 helix: 2.01 (0.15), residues: 1336 sheet: -1.48 (0.52), residues: 108 loop : -3.16 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 550 HIS 0.008 0.001 HIS A 542 PHE 0.012 0.001 PHE C 216 TYR 0.014 0.001 TYR C 78 ARG 0.006 0.000 ARG C 374 Details of bonding type rmsd hydrogen bonds : bond 0.07283 ( 960) hydrogen bonds : angle 4.21482 ( 2844) covalent geometry : bond 0.00338 (18542) covalent geometry : angle 0.61984 (25216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 2.206 Fit side-chains revert: symmetry clash REVERT: C 80 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 301 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: C 567 TYR cc_start: 0.7643 (t80) cc_final: 0.7330 (t80) REVERT: A 361 GLU cc_start: 0.7799 (tt0) cc_final: 0.6728 (pp20) REVERT: A 556 MET cc_start: 0.7383 (ttt) cc_final: 0.5974 (tmm) outliers start: 63 outliers final: 33 residues processed: 217 average time/residue: 0.3029 time to fit residues: 100.0993 Evaluate side-chains 168 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 510 ASP Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 61 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 219 optimal weight: 0.0070 chunk 177 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN A 461 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.130175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098795 restraints weight = 34606.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101675 restraints weight = 18028.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103626 restraints weight = 11540.123| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18542 Z= 0.135 Angle : 0.570 8.731 25216 Z= 0.291 Chirality : 0.039 0.172 2928 Planarity : 0.004 0.046 3206 Dihedral : 7.387 86.623 2668 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.38 % Favored : 91.53 % Rotamer: Outliers : 4.19 % Allowed : 29.22 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.19), residues: 2314 helix: 2.22 (0.15), residues: 1328 sheet: -1.56 (0.51), residues: 108 loop : -3.03 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 427 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE D 57 TYR 0.014 0.001 TYR C 55 ARG 0.003 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.06615 ( 960) hydrogen bonds : angle 3.95737 ( 2844) covalent geometry : bond 0.00273 (18542) covalent geometry : angle 0.56973 (25216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 146 time to evaluate : 2.154 Fit side-chains REVERT: C 80 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 301 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: C 407 LEU cc_start: 0.8767 (mt) cc_final: 0.8472 (mt) REVERT: C 434 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 567 TYR cc_start: 0.7648 (t80) cc_final: 0.7385 (t80) REVERT: A 16 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6313 (mp10) REVERT: A 207 ASP cc_start: 0.8276 (t0) cc_final: 0.8065 (t0) REVERT: A 361 GLU cc_start: 0.7793 (tt0) cc_final: 0.6725 (pp20) REVERT: A 456 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8149 (mp10) REVERT: A 539 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7116 (ttp) REVERT: A 556 MET cc_start: 0.7641 (ttt) cc_final: 0.6208 (tmm) outliers start: 79 outliers final: 36 residues processed: 215 average time/residue: 0.2983 time to fit residues: 99.7447 Evaluate side-chains 172 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 132 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.099312 restraints weight = 34743.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102189 restraints weight = 17971.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104147 restraints weight = 11430.193| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18542 Z= 0.128 Angle : 0.562 9.828 25216 Z= 0.284 Chirality : 0.038 0.138 2928 Planarity : 0.004 0.043 3206 Dihedral : 7.080 85.118 2668 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.64 % Favored : 91.27 % Rotamer: Outliers : 3.92 % Allowed : 29.22 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2314 helix: 2.34 (0.15), residues: 1324 sheet: -1.44 (0.50), residues: 108 loop : -3.07 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 427 HIS 0.005 0.001 HIS C 556 PHE 0.012 0.001 PHE D 57 TYR 0.013 0.001 TYR E 88 ARG 0.004 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.06263 ( 960) hydrogen bonds : angle 3.82678 ( 2844) covalent geometry : bond 0.00258 (18542) covalent geometry : angle 0.56173 (25216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 146 time to evaluate : 2.087 Fit side-chains REVERT: C 80 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7465 (tm-30) REVERT: C 102 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8760 (tppp) REVERT: C 251 MET cc_start: 0.8055 (tpp) cc_final: 0.7385 (tpp) REVERT: C 407 LEU cc_start: 0.8800 (mt) cc_final: 0.8514 (mt) REVERT: C 434 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7306 (tt) REVERT: C 524 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5977 (mmtp) REVERT: C 567 TYR cc_start: 0.7688 (t80) cc_final: 0.7454 (t80) REVERT: A 16 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6290 (mp10) REVERT: A 207 ASP cc_start: 0.8346 (t0) cc_final: 0.8111 (t0) REVERT: A 344 LEU cc_start: 0.7291 (tp) cc_final: 0.6914 (tt) REVERT: A 361 GLU cc_start: 0.7819 (tt0) cc_final: 0.6780 (pp20) REVERT: A 456 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8148 (mp10) REVERT: A 533 LEU cc_start: 0.8383 (mm) cc_final: 0.8150 (mm) REVERT: A 539 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7194 (mtp) REVERT: A 550 TRP cc_start: 0.5879 (m100) cc_final: 0.5309 (m100) REVERT: A 556 MET cc_start: 0.7616 (ttt) cc_final: 0.6272 (tmm) REVERT: D 4 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (mp) REVERT: D 534 ARG cc_start: 0.7082 (tpp-160) cc_final: 0.6581 (tpp-160) REVERT: E 384 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7588 (mtp85) outliers start: 74 outliers final: 47 residues processed: 208 average time/residue: 0.3065 time to fit residues: 97.8492 Evaluate side-chains 184 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 10 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 547 ASN A 394 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087598 restraints weight = 35378.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090213 restraints weight = 19144.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091971 restraints weight = 12562.026| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 18542 Z= 0.311 Angle : 0.733 9.085 25216 Z= 0.381 Chirality : 0.046 0.173 2928 Planarity : 0.005 0.049 3206 Dihedral : 7.563 80.479 2668 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.85 % Favored : 90.06 % Rotamer: Outliers : 5.25 % Allowed : 29.69 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.18), residues: 2314 helix: 1.45 (0.15), residues: 1346 sheet: -1.73 (0.49), residues: 114 loop : -3.17 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 550 HIS 0.007 0.001 HIS E 312 PHE 0.022 0.002 PHE C 89 TYR 0.021 0.002 TYR A 137 ARG 0.006 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.09926 ( 960) hydrogen bonds : angle 4.57289 ( 2844) covalent geometry : bond 0.00733 (18542) covalent geometry : angle 0.73313 (25216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 127 time to evaluate : 2.147 Fit side-chains REVERT: C 80 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7660 (tm-30) REVERT: C 407 LEU cc_start: 0.8765 (mt) cc_final: 0.8465 (mt) REVERT: C 434 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7374 (tt) REVERT: C 524 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5841 (mmtp) REVERT: C 567 TYR cc_start: 0.7648 (t80) cc_final: 0.7408 (t80) REVERT: A 16 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6126 (mp10) REVERT: A 159 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8104 (t80) REVERT: A 185 MET cc_start: 0.6346 (pmm) cc_final: 0.6105 (pmm) REVERT: A 207 ASP cc_start: 0.8667 (t0) cc_final: 0.8371 (t0) REVERT: A 361 GLU cc_start: 0.7994 (tt0) cc_final: 0.7751 (pt0) REVERT: A 456 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8060 (mt0) REVERT: A 533 LEU cc_start: 0.8385 (mm) cc_final: 0.8065 (mm) REVERT: A 539 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7054 (ttm) REVERT: A 550 TRP cc_start: 0.6240 (m100) cc_final: 0.5948 (m100) REVERT: A 556 MET cc_start: 0.7720 (ttt) cc_final: 0.6340 (tmm) REVERT: A 558 ASP cc_start: 0.7398 (t70) cc_final: 0.6984 (t70) REVERT: D 4 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8275 (mp) REVERT: D 534 ARG cc_start: 0.7153 (tpp-160) cc_final: 0.6848 (tpp-160) REVERT: E 159 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8241 (t80) REVERT: E 344 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7213 (tt) outliers start: 99 outliers final: 59 residues processed: 212 average time/residue: 0.2769 time to fit residues: 92.0222 Evaluate side-chains 185 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 118 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 30.0000 chunk 225 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS C 547 ASN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093755 restraints weight = 34919.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096547 restraints weight = 18338.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098432 restraints weight = 11814.077| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18542 Z= 0.143 Angle : 0.580 13.274 25216 Z= 0.297 Chirality : 0.039 0.143 2928 Planarity : 0.004 0.050 3206 Dihedral : 7.335 89.045 2668 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 4.08 % Allowed : 31.12 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.19), residues: 2314 helix: 2.00 (0.15), residues: 1330 sheet: -1.52 (0.50), residues: 114 loop : -3.11 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 550 HIS 0.002 0.001 HIS C 94 PHE 0.012 0.001 PHE D 57 TYR 0.014 0.001 TYR C 7 ARG 0.006 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.07451 ( 960) hydrogen bonds : angle 4.04347 ( 2844) covalent geometry : bond 0.00293 (18542) covalent geometry : angle 0.57980 (25216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 131 time to evaluate : 2.233 Fit side-chains REVERT: C 80 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 407 LEU cc_start: 0.8797 (mt) cc_final: 0.8494 (mt) REVERT: C 430 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8164 (tt) REVERT: C 434 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7327 (tt) REVERT: C 524 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5988 (mmtp) REVERT: C 567 TYR cc_start: 0.7641 (t80) cc_final: 0.7420 (t80) REVERT: A 16 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6250 (mp10) REVERT: A 207 ASP cc_start: 0.8672 (t0) cc_final: 0.8413 (t0) REVERT: A 456 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8145 (mp10) REVERT: A 533 LEU cc_start: 0.8388 (mm) cc_final: 0.8047 (mm) REVERT: A 556 MET cc_start: 0.7666 (ttt) cc_final: 0.6364 (tmm) REVERT: A 558 ASP cc_start: 0.7396 (t70) cc_final: 0.6987 (t70) REVERT: D 301 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8074 (t80) REVERT: D 540 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7759 (mm-40) outliers start: 77 outliers final: 46 residues processed: 196 average time/residue: 0.3050 time to fit residues: 92.6294 Evaluate side-chains 172 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 169 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091841 restraints weight = 34781.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094552 restraints weight = 18462.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096404 restraints weight = 11969.458| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18542 Z= 0.177 Angle : 0.607 13.978 25216 Z= 0.311 Chirality : 0.041 0.154 2928 Planarity : 0.004 0.047 3206 Dihedral : 7.272 85.224 2668 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.25 % Favored : 90.67 % Rotamer: Outliers : 3.92 % Allowed : 31.28 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.19), residues: 2314 helix: 1.87 (0.15), residues: 1342 sheet: -1.47 (0.49), residues: 114 loop : -3.11 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 550 HIS 0.004 0.001 HIS E 312 PHE 0.012 0.001 PHE D 57 TYR 0.015 0.001 TYR C 7 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.07911 ( 960) hydrogen bonds : angle 4.11827 ( 2844) covalent geometry : bond 0.00400 (18542) covalent geometry : angle 0.60673 (25216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 124 time to evaluate : 2.036 Fit side-chains REVERT: C 80 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 172 LEU cc_start: 0.7696 (mm) cc_final: 0.7458 (mp) REVERT: C 407 LEU cc_start: 0.8777 (mt) cc_final: 0.8479 (mt) REVERT: C 430 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8223 (tt) REVERT: C 434 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7337 (tt) REVERT: C 524 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5991 (mmtp) REVERT: C 567 TYR cc_start: 0.7647 (t80) cc_final: 0.7445 (t80) REVERT: A 16 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6161 (mp10) REVERT: A 207 ASP cc_start: 0.8705 (t0) cc_final: 0.8432 (t0) REVERT: A 441 ASP cc_start: 0.7203 (t70) cc_final: 0.6718 (m-30) REVERT: A 533 LEU cc_start: 0.8383 (mm) cc_final: 0.8008 (mm) REVERT: A 556 MET cc_start: 0.7690 (ttt) cc_final: 0.6428 (tmm) REVERT: A 558 ASP cc_start: 0.7313 (t70) cc_final: 0.6896 (t70) REVERT: A 587 GLU cc_start: 0.5396 (OUTLIER) cc_final: 0.4529 (mp0) REVERT: D 301 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8105 (t80) REVERT: E 584 ARG cc_start: 0.6352 (tpm170) cc_final: 0.5967 (tpt170) outliers start: 74 outliers final: 56 residues processed: 190 average time/residue: 0.2798 time to fit residues: 84.5234 Evaluate side-chains 181 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 34 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.123031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091437 restraints weight = 34875.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094150 restraints weight = 18511.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096020 restraints weight = 12037.246| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18542 Z= 0.176 Angle : 0.615 14.607 25216 Z= 0.314 Chirality : 0.041 0.168 2928 Planarity : 0.004 0.047 3206 Dihedral : 7.259 87.836 2668 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.29 % Favored : 90.62 % Rotamer: Outliers : 4.29 % Allowed : 31.23 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2314 helix: 1.87 (0.15), residues: 1334 sheet: -1.45 (0.49), residues: 114 loop : -3.06 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 550 HIS 0.004 0.001 HIS E 312 PHE 0.012 0.001 PHE D 57 TYR 0.015 0.001 TYR C 7 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.07963 ( 960) hydrogen bonds : angle 4.12957 ( 2844) covalent geometry : bond 0.00398 (18542) covalent geometry : angle 0.61513 (25216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 125 time to evaluate : 2.050 Fit side-chains REVERT: C 80 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7494 (tm-30) REVERT: C 172 LEU cc_start: 0.7702 (mm) cc_final: 0.7445 (mp) REVERT: C 407 LEU cc_start: 0.8774 (mt) cc_final: 0.8459 (mt) REVERT: C 430 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8254 (tt) REVERT: C 434 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7353 (tt) REVERT: C 524 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5972 (mmtp) REVERT: C 567 TYR cc_start: 0.7672 (t80) cc_final: 0.7470 (t80) REVERT: A 16 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: A 207 ASP cc_start: 0.8715 (t0) cc_final: 0.8460 (t0) REVERT: A 441 ASP cc_start: 0.7258 (t70) cc_final: 0.6800 (m-30) REVERT: A 521 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5518 (pp20) REVERT: A 533 LEU cc_start: 0.8385 (mm) cc_final: 0.8104 (mm) REVERT: A 539 MET cc_start: 0.7501 (ttm) cc_final: 0.7256 (ttp) REVERT: A 558 ASP cc_start: 0.7355 (t70) cc_final: 0.6949 (t70) REVERT: A 587 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4553 (mp0) REVERT: D 60 MET cc_start: 0.8280 (tpp) cc_final: 0.8022 (tmm) REVERT: D 97 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (mp) REVERT: D 301 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8074 (t80) REVERT: D 540 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: E 159 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8177 (t80) REVERT: E 584 ARG cc_start: 0.6476 (tpm170) cc_final: 0.6026 (tpt170) outliers start: 81 outliers final: 58 residues processed: 198 average time/residue: 0.2695 time to fit residues: 84.9560 Evaluate side-chains 185 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 117 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 180 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092678 restraints weight = 34859.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095425 restraints weight = 18390.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097260 restraints weight = 11920.033| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18542 Z= 0.155 Angle : 0.600 14.887 25216 Z= 0.306 Chirality : 0.040 0.184 2928 Planarity : 0.004 0.048 3206 Dihedral : 7.183 89.676 2668 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.95 % Favored : 90.97 % Rotamer: Outliers : 4.19 % Allowed : 31.18 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.19), residues: 2314 helix: 1.97 (0.15), residues: 1326 sheet: -1.39 (0.49), residues: 114 loop : -3.10 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 550 HIS 0.003 0.001 HIS E 312 PHE 0.026 0.001 PHE D 539 TYR 0.013 0.001 TYR A 88 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.07548 ( 960) hydrogen bonds : angle 4.03548 ( 2844) covalent geometry : bond 0.00333 (18542) covalent geometry : angle 0.59996 (25216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 121 time to evaluate : 2.253 Fit side-chains REVERT: C 80 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 172 LEU cc_start: 0.7687 (mm) cc_final: 0.7426 (mp) REVERT: C 407 LEU cc_start: 0.8763 (mt) cc_final: 0.8449 (mt) REVERT: C 430 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8242 (tt) REVERT: C 434 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7372 (tt) REVERT: C 524 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5934 (mmtp) REVERT: A 16 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6293 (mp10) REVERT: A 207 ASP cc_start: 0.8676 (t0) cc_final: 0.8424 (t0) REVERT: A 441 ASP cc_start: 0.7181 (t70) cc_final: 0.6749 (m-30) REVERT: A 533 LEU cc_start: 0.8420 (mm) cc_final: 0.8118 (mm) REVERT: A 539 MET cc_start: 0.7441 (ttm) cc_final: 0.7234 (ttp) REVERT: A 558 ASP cc_start: 0.7291 (t70) cc_final: 0.6886 (t70) REVERT: A 572 VAL cc_start: 0.6524 (OUTLIER) cc_final: 0.6246 (t) REVERT: A 587 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.4569 (mp0) REVERT: D 97 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8543 (mp) REVERT: D 301 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8054 (t80) REVERT: E 159 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8119 (t80) outliers start: 79 outliers final: 58 residues processed: 194 average time/residue: 0.2791 time to fit residues: 85.8280 Evaluate side-chains 185 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 118 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 0.0010 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 167 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094311 restraints weight = 34747.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097080 restraints weight = 18320.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.098986 restraints weight = 11837.831| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18542 Z= 0.142 Angle : 0.601 15.508 25216 Z= 0.303 Chirality : 0.039 0.172 2928 Planarity : 0.004 0.042 3206 Dihedral : 7.098 88.682 2668 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 3.45 % Allowed : 31.97 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2314 helix: 2.04 (0.15), residues: 1332 sheet: -1.35 (0.49), residues: 114 loop : -3.07 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 550 HIS 0.003 0.001 HIS E 312 PHE 0.010 0.001 PHE D 145 TYR 0.023 0.001 TYR C 567 ARG 0.005 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.07134 ( 960) hydrogen bonds : angle 3.95453 ( 2844) covalent geometry : bond 0.00295 (18542) covalent geometry : angle 0.60137 (25216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 2.076 Fit side-chains REVERT: C 80 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 172 LEU cc_start: 0.7666 (mm) cc_final: 0.7408 (mp) REVERT: C 407 LEU cc_start: 0.8770 (mt) cc_final: 0.8443 (mt) REVERT: C 430 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (tt) REVERT: C 524 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5918 (mmtp) REVERT: A 16 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6239 (mp10) REVERT: A 207 ASP cc_start: 0.8660 (t0) cc_final: 0.8401 (t0) REVERT: A 441 ASP cc_start: 0.7161 (t70) cc_final: 0.6731 (m-30) REVERT: A 521 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.5494 (pp20) REVERT: A 533 LEU cc_start: 0.8407 (mm) cc_final: 0.8107 (mm) REVERT: A 558 ASP cc_start: 0.7283 (t70) cc_final: 0.6871 (t70) REVERT: A 572 VAL cc_start: 0.6628 (OUTLIER) cc_final: 0.6425 (t) REVERT: A 587 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4562 (mp0) REVERT: D 97 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 301 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8040 (t80) REVERT: D 540 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7684 (mm-40) REVERT: E 159 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8123 (t80) REVERT: E 584 ARG cc_start: 0.5578 (tpt170) cc_final: 0.5336 (tpt170) outliers start: 65 outliers final: 54 residues processed: 181 average time/residue: 0.2911 time to fit residues: 83.6092 Evaluate side-chains 182 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 542 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095172 restraints weight = 34650.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097970 restraints weight = 18177.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099861 restraints weight = 11684.293| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18542 Z= 0.138 Angle : 0.597 15.511 25216 Z= 0.299 Chirality : 0.039 0.161 2928 Planarity : 0.004 0.053 3206 Dihedral : 6.952 89.049 2668 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.77 % Favored : 91.14 % Rotamer: Outliers : 3.66 % Allowed : 31.81 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.19), residues: 2314 helix: 2.11 (0.15), residues: 1332 sheet: -1.31 (0.49), residues: 114 loop : -3.06 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 550 HIS 0.003 0.001 HIS E 312 PHE 0.010 0.001 PHE D 145 TYR 0.019 0.001 TYR C 567 ARG 0.013 0.000 ARG C 565 Details of bonding type rmsd hydrogen bonds : bond 0.06758 ( 960) hydrogen bonds : angle 3.87997 ( 2844) covalent geometry : bond 0.00291 (18542) covalent geometry : angle 0.59718 (25216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5758.05 seconds wall clock time: 100 minutes 18.95 seconds (6018.95 seconds total)