Starting phenix.real_space_refine on Thu Feb 15 15:42:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/02_2024/7n6r_24209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/02_2024/7n6r_24209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/02_2024/7n6r_24209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/02_2024/7n6r_24209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/02_2024/7n6r_24209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6r_24209/02_2024/7n6r_24209_updated.pdb" } resolution = 3.93 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= 0.005 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 8656 2.51 5 N 2004 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12708 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "B" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "C" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "D" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.18, per 1000 atoms: 0.56 Number of scatterers: 12708 At special positions: 0 Unit cell: (112.455, 184.093, 74.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 1948 8.00 N 2004 7.00 C 8656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 0 sheets defined 70.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 118 through 142 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 163 through 188 Proline residue: A 172 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.805A pdb=" N ALA A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 226 through 254 removed outlier: 4.340A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.597A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.745A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.890A pdb=" N ARG A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.634A pdb=" N HIS A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 Processing helix chain 'A' and resid 473 through 498 removed outlier: 4.547A pdb=" N LEU A 483 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 487 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 491 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 496 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 118 through 143 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 163 through 188 Proline residue: B 172 - end of helix Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.821A pdb=" N ALA B 205 " --> pdb=" O CYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 226 through 254 removed outlier: 4.039A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 268 through 276 removed outlier: 3.629A pdb=" N PHE B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 317 Processing helix chain 'B' and resid 320 through 323 No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.727A pdb=" N LEU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 387 through 393 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.893A pdb=" N ARG B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 422 No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 425 through 441 removed outlier: 3.581A pdb=" N HIS B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 461 Processing helix chain 'B' and resid 473 through 498 removed outlier: 4.573A pdb=" N LEU B 483 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE B 487 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 491 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP B 496 " --> pdb=" O CYS B 493 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 118 through 143 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 172 - end of helix Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.803A pdb=" N ALA C 205 " --> pdb=" O CYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 226 through 254 removed outlier: 4.319A pdb=" N LEU C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Proline residue: C 252 - end of helix Processing helix chain 'C' and resid 268 through 276 removed outlier: 3.604A pdb=" N PHE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 317 Processing helix chain 'C' and resid 320 through 323 No H-bonds generated for 'chain 'C' and resid 320 through 323' Processing helix chain 'C' and resid 334 through 342 removed outlier: 3.751A pdb=" N LEU C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 407 through 414 removed outlier: 3.904A pdb=" N ARG C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 422 No H-bonds generated for 'chain 'C' and resid 419 through 422' Processing helix chain 'C' and resid 425 through 441 removed outlier: 3.627A pdb=" N HIS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 461 Processing helix chain 'C' and resid 473 through 498 removed outlier: 4.554A pdb=" N LEU C 483 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 487 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 491 " --> pdb=" O GLN C 488 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN C 494 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP C 496 " --> pdb=" O CYS C 493 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 118 through 143 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 172 - end of helix Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.824A pdb=" N ALA D 205 " --> pdb=" O CYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 220 Processing helix chain 'D' and resid 226 through 254 removed outlier: 4.040A pdb=" N LEU D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Proline residue: D 252 - end of helix Processing helix chain 'D' and resid 268 through 276 removed outlier: 3.630A pdb=" N PHE D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 317 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 334 through 342 removed outlier: 3.729A pdb=" N LEU D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 359 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 387 through 393 Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 407 through 414 removed outlier: 3.895A pdb=" N ARG D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 425 through 441 removed outlier: 3.579A pdb=" N HIS D 434 " --> pdb=" O SER D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 Processing helix chain 'D' and resid 473 through 498 removed outlier: 4.582A pdb=" N LEU D 483 " --> pdb=" O MET D 480 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE D 487 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 489 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 491 " --> pdb=" O GLN D 488 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN D 494 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP D 496 " --> pdb=" O CYS D 493 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1767 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: 3.44 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1976 1.33 - 1.45: 3818 1.45 - 1.57: 7154 1.57 - 1.69: 16 1.69 - 1.82: 156 Bond restraints: 13120 Sorted by residual: bond pdb=" C19 ROV D 601 " pdb=" C20 ROV D 601 " ideal model delta sigma weight residual 1.534 1.367 0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C19 ROV A 601 " pdb=" C20 ROV A 601 " ideal model delta sigma weight residual 1.534 1.367 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C19 ROV B 601 " pdb=" C20 ROV B 601 " ideal model delta sigma weight residual 1.534 1.368 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C19 ROV C 601 " pdb=" C20 ROV C 601 " ideal model delta sigma weight residual 1.534 1.368 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C18 ROV C 601 " pdb=" C22 ROV C 601 " ideal model delta sigma weight residual 1.538 1.374 0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.72: 343 105.72 - 112.99: 6618 112.99 - 120.25: 5993 120.25 - 127.52: 4767 127.52 - 134.79: 143 Bond angle restraints: 17864 Sorted by residual: angle pdb=" C GLY D 457 " pdb=" N GLY D 458 " pdb=" CA GLY D 458 " ideal model delta sigma weight residual 120.03 125.62 -5.59 1.12e+00 7.97e-01 2.49e+01 angle pdb=" C GLY B 457 " pdb=" N GLY B 458 " pdb=" CA GLY B 458 " ideal model delta sigma weight residual 120.03 125.60 -5.57 1.12e+00 7.97e-01 2.47e+01 angle pdb=" C GLY A 457 " pdb=" N GLY A 458 " pdb=" CA GLY A 458 " ideal model delta sigma weight residual 120.03 125.60 -5.57 1.12e+00 7.97e-01 2.47e+01 angle pdb=" C GLY C 457 " pdb=" N GLY C 458 " pdb=" CA GLY C 458 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.46e+01 angle pdb=" C LEU A 199 " pdb=" N GLY A 200 " pdb=" CA GLY A 200 " ideal model delta sigma weight residual 120.03 125.12 -5.09 1.12e+00 7.97e-01 2.07e+01 ... (remaining 17859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6961 17.71 - 35.41: 693 35.41 - 53.12: 170 53.12 - 70.83: 34 70.83 - 88.53: 18 Dihedral angle restraints: 7876 sinusoidal: 3468 harmonic: 4408 Sorted by residual: dihedral pdb=" CA VAL D 117 " pdb=" C VAL D 117 " pdb=" N GLN D 118 " pdb=" CA GLN D 118 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA VAL C 117 " pdb=" C VAL C 117 " pdb=" N GLN C 118 " pdb=" CA GLN C 118 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL B 117 " pdb=" C VAL B 117 " pdb=" N GLN B 118 " pdb=" CA GLN B 118 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1009 0.058 - 0.116: 715 0.116 - 0.173: 233 0.173 - 0.231: 15 0.231 - 0.289: 12 Chirality restraints: 1984 Sorted by residual: chirality pdb=" C13 CLR A 603 " pdb=" C12 CLR A 603 " pdb=" C14 CLR A 603 " pdb=" C17 CLR A 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C13 CLR D 602 " pdb=" C12 CLR D 602 " pdb=" C14 CLR D 602 " pdb=" C17 CLR D 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C13 CLR B 603 " pdb=" C12 CLR B 603 " pdb=" C14 CLR B 603 " pdb=" C17 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1981 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 490 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C SER A 490 " -0.035 2.00e-02 2.50e+03 pdb=" O SER A 490 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 491 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 490 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C SER C 490 " 0.035 2.00e-02 2.50e+03 pdb=" O SER C 490 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU C 491 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 490 " -0.009 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C SER B 490 " 0.034 2.00e-02 2.50e+03 pdb=" O SER B 490 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 491 " -0.012 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1365 2.79 - 3.32: 13499 3.32 - 3.85: 19629 3.85 - 4.37: 24359 4.37 - 4.90: 40099 Nonbonded interactions: 98951 Sorted by model distance: nonbonded pdb=" O ILE C 281 " pdb=" OH TYR C 286 " model vdw 2.264 2.440 nonbonded pdb=" O ILE A 281 " pdb=" OH TYR A 286 " model vdw 2.264 2.440 nonbonded pdb=" O ILE D 281 " pdb=" OH TYR D 286 " model vdw 2.282 2.440 nonbonded pdb=" O ILE B 281 " pdb=" OH TYR B 286 " model vdw 2.283 2.440 nonbonded pdb=" NE2 GLN D 236 " pdb=" OH TYR D 436 " model vdw 2.395 2.520 ... (remaining 98946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.960 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.240 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.015 0.167 13120 Z= 1.007 Angle : 1.794 7.702 17864 Z= 1.333 Chirality : 0.078 0.289 1984 Planarity : 0.004 0.020 2108 Dihedral : 15.717 88.533 5028 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.14 % Favored : 94.59 % Rotamer: Outliers : 1.24 % Allowed : 8.20 % Favored : 90.56 % 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: -3.93 (0.18), residues: 1460 helix: -2.25 (0.13), residues: 1044 sheet: None (None), residues: 0 loop : -3.07 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 401 HIS 0.008 0.002 HIS C 119 PHE 0.028 0.003 PHE C 444 TYR 0.020 0.003 TYR A 271 ARG 0.003 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 393 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8215 (mt0) cc_final: 0.7946 (mp10) REVERT: A 122 THR cc_start: 0.8837 (m) cc_final: 0.8574 (m) REVERT: A 135 ILE cc_start: 0.7723 (tt) cc_final: 0.7488 (tt) REVERT: A 284 GLU cc_start: 0.8457 (pp20) cc_final: 0.7832 (pt0) REVERT: A 374 ASP cc_start: 0.7715 (t0) cc_final: 0.7342 (t0) REVERT: A 442 LEU cc_start: 0.8203 (mt) cc_final: 0.7987 (mt) REVERT: A 444 PHE cc_start: 0.6957 (m-80) cc_final: 0.6523 (m-80) REVERT: A 480 MET cc_start: 0.7851 (mmt) cc_final: 0.7094 (tmm) REVERT: B 169 THR cc_start: 0.8313 (t) cc_final: 0.8077 (p) REVERT: B 170 TRP cc_start: 0.8127 (t60) cc_final: 0.7351 (t60) REVERT: B 247 LEU cc_start: 0.9193 (mm) cc_final: 0.8805 (tt) REVERT: B 274 PHE cc_start: 0.8400 (t80) cc_final: 0.8134 (t80) REVERT: B 350 MET cc_start: 0.7928 (mmm) cc_final: 0.6976 (tmm) REVERT: B 360 HIS cc_start: 0.8052 (t70) cc_final: 0.7311 (t70) REVERT: B 380 ASP cc_start: 0.7305 (p0) cc_final: 0.6611 (p0) REVERT: B 381 TRP cc_start: 0.9071 (p-90) cc_final: 0.8842 (p-90) REVERT: B 393 THR cc_start: 0.8673 (p) cc_final: 0.7810 (t) REVERT: B 419 ARG cc_start: 0.5983 (ptt-90) cc_final: 0.4807 (ptm160) REVERT: B 423 MET cc_start: 0.8165 (ttp) cc_final: 0.7944 (tpp) REVERT: B 435 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: B 473 TRP cc_start: 0.7827 (t-100) cc_final: 0.6694 (m-90) REVERT: C 115 MET cc_start: 0.8317 (tpt) cc_final: 0.8111 (tpt) REVERT: C 374 ASP cc_start: 0.7769 (t0) cc_final: 0.7198 (t0) REVERT: C 444 PHE cc_start: 0.7026 (m-80) cc_final: 0.6510 (m-80) REVERT: D 102 LYS cc_start: 0.7984 (tttm) cc_final: 0.7476 (tppt) REVERT: D 170 TRP cc_start: 0.8076 (t60) cc_final: 0.7051 (t60) REVERT: D 247 LEU cc_start: 0.9139 (mm) cc_final: 0.8730 (tt) REVERT: D 266 PRO cc_start: 0.7397 (Cg_endo) cc_final: 0.6564 (Cg_exo) REVERT: D 379 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7043 (mtp85) REVERT: D 380 ASP cc_start: 0.6825 (p0) cc_final: 0.6510 (p0) REVERT: D 391 TYR cc_start: 0.7876 (m-80) cc_final: 0.7487 (t80) REVERT: D 393 THR cc_start: 0.8475 (p) cc_final: 0.7616 (t) REVERT: D 428 LEU cc_start: 0.8825 (tp) cc_final: 0.8594 (pp) REVERT: D 435 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: D 473 TRP cc_start: 0.7937 (t-100) cc_final: 0.6625 (m-90) REVERT: D 476 LEU cc_start: 0.8259 (tt) cc_final: 0.7426 (mm) outliers start: 16 outliers final: 3 residues processed: 401 average time/residue: 0.2460 time to fit residues: 139.9621 Evaluate side-chains 273 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 435 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 236 GLN B 207 HIS B 217 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN C 207 HIS C 236 GLN D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13120 Z= 0.196 Angle : 0.695 10.453 17864 Z= 0.329 Chirality : 0.040 0.143 1984 Planarity : 0.004 0.038 2108 Dihedral : 9.344 85.660 2330 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.02 % Allowed : 19.81 % Favored : 76.16 % 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: -1.21 (0.22), residues: 1460 helix: -0.10 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 188 HIS 0.005 0.001 HIS D 217 PHE 0.013 0.001 PHE B 143 TYR 0.020 0.001 TYR C 124 ARG 0.004 0.000 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 309 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8311 (mt0) cc_final: 0.7916 (mp10) REVERT: A 122 THR cc_start: 0.8664 (m) cc_final: 0.8410 (m) REVERT: A 135 ILE cc_start: 0.7529 (tt) cc_final: 0.7322 (tt) REVERT: A 368 GLU cc_start: 0.8072 (tp30) cc_final: 0.7765 (tp30) REVERT: A 376 MET cc_start: 0.7993 (tpp) cc_final: 0.7732 (ttp) REVERT: A 391 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7108 (t80) REVERT: A 444 PHE cc_start: 0.7935 (m-80) cc_final: 0.7299 (m-80) REVERT: A 462 PHE cc_start: 0.7371 (m-10) cc_final: 0.7170 (m-10) REVERT: B 247 LEU cc_start: 0.9279 (mm) cc_final: 0.8741 (tt) REVERT: B 281 ILE cc_start: 0.8213 (mm) cc_final: 0.7595 (tp) REVERT: B 300 ASN cc_start: 0.7326 (t0) cc_final: 0.6528 (t0) REVERT: B 350 MET cc_start: 0.7917 (mmm) cc_final: 0.7300 (mpp) REVERT: B 360 HIS cc_start: 0.8122 (t70) cc_final: 0.7675 (t70) REVERT: B 379 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7528 (mtm110) REVERT: B 396 VAL cc_start: 0.6903 (t) cc_final: 0.6681 (p) REVERT: B 419 ARG cc_start: 0.5713 (ptt-90) cc_final: 0.4609 (ptm160) REVERT: B 453 PHE cc_start: 0.7794 (t80) cc_final: 0.7478 (t80) REVERT: B 473 TRP cc_start: 0.8023 (t-100) cc_final: 0.6820 (m-90) REVERT: C 122 THR cc_start: 0.8617 (m) cc_final: 0.8390 (m) REVERT: C 188 TRP cc_start: 0.6688 (t-100) cc_final: 0.6430 (t-100) REVERT: C 374 ASP cc_start: 0.7683 (t0) cc_final: 0.7388 (t0) REVERT: C 391 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7243 (t80) REVERT: C 444 PHE cc_start: 0.7979 (m-80) cc_final: 0.7159 (m-80) REVERT: C 459 MET cc_start: 0.4716 (ttm) cc_final: 0.4506 (ttt) REVERT: D 126 MET cc_start: 0.7602 (ttp) cc_final: 0.7344 (ttm) REVERT: D 169 THR cc_start: 0.8089 (m) cc_final: 0.7865 (p) REVERT: D 170 TRP cc_start: 0.8181 (t60) cc_final: 0.6965 (t60) REVERT: D 224 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8065 (mm) REVERT: D 247 LEU cc_start: 0.9144 (mm) cc_final: 0.8597 (tt) REVERT: D 286 TYR cc_start: 0.7099 (m-10) cc_final: 0.6497 (m-10) REVERT: D 376 MET cc_start: 0.6730 (tpp) cc_final: 0.6419 (tpt) REVERT: D 408 GLN cc_start: 0.8143 (mt0) cc_final: 0.7868 (mm-40) REVERT: D 473 TRP cc_start: 0.8025 (t-100) cc_final: 0.6765 (m-90) REVERT: D 476 LEU cc_start: 0.7840 (tt) cc_final: 0.7610 (tp) outliers start: 52 outliers final: 28 residues processed: 338 average time/residue: 0.2141 time to fit residues: 107.0786 Evaluate side-chains 300 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 269 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 217 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN D 399 HIS D 434 HIS ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 13120 Z= 0.453 Angle : 0.855 11.365 17864 Z= 0.410 Chirality : 0.049 0.257 1984 Planarity : 0.005 0.041 2108 Dihedral : 8.646 59.326 2316 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 6.50 % Allowed : 23.61 % Favored : 69.89 % 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: -1.16 (0.21), residues: 1460 helix: -0.01 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -2.68 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 394 HIS 0.011 0.002 HIS C 399 PHE 0.026 0.002 PHE C 453 TYR 0.022 0.002 TYR C 446 ARG 0.005 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 298 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8433 (mt0) cc_final: 0.8036 (mp10) REVERT: A 122 THR cc_start: 0.8802 (m) cc_final: 0.8548 (m) REVERT: A 142 ASP cc_start: 0.7141 (m-30) cc_final: 0.6899 (m-30) REVERT: A 223 GLN cc_start: 0.6970 (mt0) cc_final: 0.6117 (pp30) REVERT: A 284 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 350 MET cc_start: 0.7056 (tpt) cc_final: 0.6728 (mmm) REVERT: A 391 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7437 (t80) REVERT: A 444 PHE cc_start: 0.8314 (m-80) cc_final: 0.7665 (m-80) REVERT: B 115 MET cc_start: 0.7884 (tpt) cc_final: 0.7638 (tpt) REVERT: B 142 ASP cc_start: 0.7037 (m-30) cc_final: 0.6619 (t0) REVERT: B 170 TRP cc_start: 0.8095 (t60) cc_final: 0.7132 (t60) REVERT: B 224 LEU cc_start: 0.8693 (mm) cc_final: 0.8165 (mm) REVERT: B 235 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8141 (mm-30) REVERT: B 247 LEU cc_start: 0.9301 (mm) cc_final: 0.8710 (tt) REVERT: B 300 ASN cc_start: 0.7565 (m-40) cc_final: 0.6690 (t0) REVERT: B 350 MET cc_start: 0.7922 (mmm) cc_final: 0.7405 (mpp) REVERT: B 379 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7115 (mtp85) REVERT: B 393 THR cc_start: 0.8560 (p) cc_final: 0.7848 (t) REVERT: B 419 ARG cc_start: 0.5624 (ptt-90) cc_final: 0.4385 (ptm160) REVERT: B 473 TRP cc_start: 0.8115 (t-100) cc_final: 0.7356 (t-100) REVERT: B 492 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: C 122 THR cc_start: 0.8687 (m) cc_final: 0.8436 (m) REVERT: C 223 GLN cc_start: 0.7014 (mt0) cc_final: 0.6153 (pp30) REVERT: C 286 TYR cc_start: 0.8425 (m-10) cc_final: 0.8195 (m-80) REVERT: C 350 MET cc_start: 0.6896 (tpt) cc_final: 0.6586 (mmm) REVERT: C 391 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7600 (t80) REVERT: C 444 PHE cc_start: 0.7953 (m-80) cc_final: 0.7371 (m-80) REVERT: C 449 MET cc_start: 0.8084 (ttt) cc_final: 0.7700 (tpt) REVERT: C 463 MET cc_start: 0.5228 (mtm) cc_final: 0.5016 (mtm) REVERT: D 126 MET cc_start: 0.7501 (ttp) cc_final: 0.7270 (ttm) REVERT: D 142 ASP cc_start: 0.7469 (m-30) cc_final: 0.7165 (t0) REVERT: D 224 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (mm) REVERT: D 235 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7895 (tp30) REVERT: D 247 LEU cc_start: 0.9194 (mm) cc_final: 0.8587 (tt) REVERT: D 408 GLN cc_start: 0.8377 (mt0) cc_final: 0.7830 (mm-40) REVERT: D 453 PHE cc_start: 0.7922 (t80) cc_final: 0.7480 (t80) REVERT: D 473 TRP cc_start: 0.7967 (t-100) cc_final: 0.7648 (t-100) outliers start: 84 outliers final: 54 residues processed: 342 average time/residue: 0.2103 time to fit residues: 107.2325 Evaluate side-chains 326 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 268 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 236 GLN A 342 HIS B 217 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13120 Z= 0.172 Angle : 0.667 10.225 17864 Z= 0.306 Chirality : 0.040 0.199 1984 Planarity : 0.004 0.045 2108 Dihedral : 7.655 59.165 2316 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.42 % Allowed : 25.93 % Favored : 68.65 % 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: -0.66 (0.22), residues: 1460 helix: 0.37 (0.16), residues: 1084 sheet: None (None), residues: 0 loop : -2.73 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 294 HIS 0.003 0.001 HIS B 217 PHE 0.011 0.001 PHE D 440 TYR 0.017 0.001 TYR B 182 ARG 0.005 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 278 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8452 (mt0) cc_final: 0.8033 (mp10) REVERT: A 122 THR cc_start: 0.8786 (m) cc_final: 0.8530 (m) REVERT: A 135 ILE cc_start: 0.7618 (tt) cc_final: 0.7404 (tt) REVERT: A 223 GLN cc_start: 0.6991 (mt0) cc_final: 0.6226 (pp30) REVERT: A 286 TYR cc_start: 0.7603 (m-80) cc_final: 0.7359 (m-80) REVERT: A 338 LEU cc_start: 0.7916 (tp) cc_final: 0.7399 (tp) REVERT: A 342 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.5715 (m90) REVERT: A 368 GLU cc_start: 0.8064 (tp30) cc_final: 0.7606 (tp30) REVERT: A 375 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7541 (mtt-85) REVERT: A 444 PHE cc_start: 0.8263 (m-80) cc_final: 0.7661 (m-80) REVERT: B 142 ASP cc_start: 0.7004 (m-30) cc_final: 0.6533 (t0) REVERT: B 224 LEU cc_start: 0.8658 (mm) cc_final: 0.8193 (mm) REVERT: B 247 LEU cc_start: 0.9231 (mm) cc_final: 0.8614 (tt) REVERT: B 281 ILE cc_start: 0.8355 (mm) cc_final: 0.7910 (tp) REVERT: B 283 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8254 (mmt90) REVERT: B 300 ASN cc_start: 0.7250 (m-40) cc_final: 0.6546 (t0) REVERT: B 350 MET cc_start: 0.7920 (mmm) cc_final: 0.7380 (tpp) REVERT: B 419 ARG cc_start: 0.5444 (ptt-90) cc_final: 0.4131 (ptm160) REVERT: B 453 PHE cc_start: 0.7782 (t80) cc_final: 0.7400 (t80) REVERT: B 473 TRP cc_start: 0.8046 (t-100) cc_final: 0.7705 (t-100) REVERT: B 495 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4291 (mp0) REVERT: C 122 THR cc_start: 0.8640 (m) cc_final: 0.8391 (m) REVERT: C 135 ILE cc_start: 0.7707 (tt) cc_final: 0.7507 (tt) REVERT: C 286 TYR cc_start: 0.8092 (m-10) cc_final: 0.7814 (m-80) REVERT: C 391 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 424 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6665 (mm) REVERT: C 444 PHE cc_start: 0.7968 (m-10) cc_final: 0.7464 (m-80) REVERT: D 115 MET cc_start: 0.8114 (tpt) cc_final: 0.7683 (tpt) REVERT: D 126 MET cc_start: 0.7572 (ttp) cc_final: 0.7350 (ttm) REVERT: D 142 ASP cc_start: 0.7332 (m-30) cc_final: 0.7074 (t0) REVERT: D 300 ASN cc_start: 0.6720 (t0) cc_final: 0.6255 (t0) REVERT: D 394 TRP cc_start: 0.7345 (t-100) cc_final: 0.6964 (t-100) REVERT: D 408 GLN cc_start: 0.8331 (mt0) cc_final: 0.7772 (mm-40) REVERT: D 453 PHE cc_start: 0.7447 (t80) cc_final: 0.7231 (t80) REVERT: D 473 TRP cc_start: 0.7939 (t-100) cc_final: 0.7632 (t-100) outliers start: 70 outliers final: 47 residues processed: 320 average time/residue: 0.2235 time to fit residues: 106.7070 Evaluate side-chains 316 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 265 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 20.0000 chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 342 HIS B 217 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13120 Z= 0.222 Angle : 0.676 11.227 17864 Z= 0.312 Chirality : 0.041 0.187 1984 Planarity : 0.004 0.042 2108 Dihedral : 7.413 57.758 2316 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.11 % Allowed : 25.31 % Favored : 68.58 % 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: -0.52 (0.22), residues: 1460 helix: 0.46 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.69 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 478 HIS 0.008 0.001 HIS A 342 PHE 0.013 0.001 PHE D 440 TYR 0.019 0.001 TYR B 182 ARG 0.004 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 272 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8524 (mt0) cc_final: 0.8039 (mp10) REVERT: A 115 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.6573 (mpm) REVERT: A 122 THR cc_start: 0.8752 (m) cc_final: 0.8484 (m) REVERT: A 223 GLN cc_start: 0.7037 (mt0) cc_final: 0.6304 (pp30) REVERT: A 342 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6179 (m90) REVERT: A 350 MET cc_start: 0.6913 (tpt) cc_final: 0.6563 (mmm) REVERT: A 375 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7599 (mtt-85) REVERT: B 142 ASP cc_start: 0.7020 (m-30) cc_final: 0.6551 (t0) REVERT: B 224 LEU cc_start: 0.8696 (mm) cc_final: 0.8218 (mm) REVERT: B 235 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 241 MET cc_start: 0.8449 (mtt) cc_final: 0.7974 (mmt) REVERT: B 247 LEU cc_start: 0.9226 (mm) cc_final: 0.8594 (tt) REVERT: B 281 ILE cc_start: 0.8410 (mm) cc_final: 0.7827 (tp) REVERT: B 283 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8268 (mmt90) REVERT: B 300 ASN cc_start: 0.7252 (m-40) cc_final: 0.6545 (t0) REVERT: B 350 MET cc_start: 0.7910 (mmm) cc_final: 0.7636 (tpp) REVERT: B 419 ARG cc_start: 0.5390 (ptt-90) cc_final: 0.4025 (ptm160) REVERT: B 473 TRP cc_start: 0.8025 (t-100) cc_final: 0.7688 (t-100) REVERT: B 492 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: B 495 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.4198 (mp0) REVERT: C 115 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.6667 (mpm) REVERT: C 122 THR cc_start: 0.8619 (m) cc_final: 0.8357 (m) REVERT: C 188 TRP cc_start: 0.6523 (m-10) cc_final: 0.6231 (m-10) REVERT: C 223 GLN cc_start: 0.6945 (mt0) cc_final: 0.6155 (pp30) REVERT: C 286 TYR cc_start: 0.8188 (m-10) cc_final: 0.7909 (m-80) REVERT: C 391 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7347 (t80) REVERT: C 444 PHE cc_start: 0.8045 (m-10) cc_final: 0.7288 (m-10) REVERT: C 463 MET cc_start: 0.5233 (mtm) cc_final: 0.5030 (mtm) REVERT: C 495 GLU cc_start: 0.7109 (tp30) cc_final: 0.6660 (tm-30) REVERT: D 126 MET cc_start: 0.7584 (ttp) cc_final: 0.7376 (ttm) REVERT: D 142 ASP cc_start: 0.7267 (m-30) cc_final: 0.7062 (t0) REVERT: D 207 HIS cc_start: 0.9010 (t-90) cc_final: 0.8588 (t-90) REVERT: D 247 LEU cc_start: 0.9106 (mm) cc_final: 0.8497 (tt) REVERT: D 300 ASN cc_start: 0.6793 (t0) cc_final: 0.6312 (t0) REVERT: D 326 MET cc_start: 0.5753 (tmm) cc_final: 0.4964 (ppp) REVERT: D 408 GLN cc_start: 0.8322 (mt0) cc_final: 0.7726 (mm-40) REVERT: D 453 PHE cc_start: 0.7534 (t80) cc_final: 0.7330 (t80) REVERT: D 473 TRP cc_start: 0.7946 (t-100) cc_final: 0.7688 (t-100) outliers start: 79 outliers final: 51 residues processed: 326 average time/residue: 0.2209 time to fit residues: 108.4831 Evaluate side-chains 313 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 256 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 119 HIS B 217 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13120 Z= 0.280 Angle : 0.716 11.960 17864 Z= 0.332 Chirality : 0.043 0.211 1984 Planarity : 0.005 0.042 2108 Dihedral : 7.488 58.961 2316 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.12 % Allowed : 25.00 % Favored : 67.88 % 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: -0.55 (0.22), residues: 1460 helix: 0.44 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.69 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 478 HIS 0.012 0.001 HIS A 342 PHE 0.014 0.001 PHE C 453 TYR 0.019 0.001 TYR B 182 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 262 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8507 (mt0) cc_final: 0.8074 (mp10) REVERT: A 115 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.6706 (mpm) REVERT: A 122 THR cc_start: 0.8776 (m) cc_final: 0.8516 (m) REVERT: A 153 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: A 223 GLN cc_start: 0.7068 (mt0) cc_final: 0.6356 (pp30) REVERT: A 338 LEU cc_start: 0.8024 (tp) cc_final: 0.7797 (tp) REVERT: A 342 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6410 (m-70) REVERT: A 350 MET cc_start: 0.6976 (tpt) cc_final: 0.6639 (mmm) REVERT: A 394 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7278 (t-100) REVERT: B 142 ASP cc_start: 0.7030 (m-30) cc_final: 0.6607 (t0) REVERT: B 224 LEU cc_start: 0.8744 (mm) cc_final: 0.8256 (mm) REVERT: B 247 LEU cc_start: 0.9208 (mm) cc_final: 0.8591 (tt) REVERT: B 281 ILE cc_start: 0.8460 (mm) cc_final: 0.7872 (tp) REVERT: B 283 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8172 (mmt90) REVERT: B 300 ASN cc_start: 0.7341 (m-40) cc_final: 0.6583 (t0) REVERT: B 350 MET cc_start: 0.7933 (mmm) cc_final: 0.7649 (tpp) REVERT: B 419 ARG cc_start: 0.5422 (ptt-90) cc_final: 0.4032 (ptm160) REVERT: B 473 TRP cc_start: 0.8017 (t-100) cc_final: 0.7671 (t-100) REVERT: B 492 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: B 495 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4238 (mp0) REVERT: C 115 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.6618 (mpm) REVERT: C 122 THR cc_start: 0.8628 (m) cc_final: 0.8368 (m) REVERT: C 153 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: C 188 TRP cc_start: 0.6825 (m-10) cc_final: 0.6526 (m-10) REVERT: C 221 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7575 (tt0) REVERT: C 223 GLN cc_start: 0.6975 (mt0) cc_final: 0.6193 (pp30) REVERT: C 286 TYR cc_start: 0.8156 (m-10) cc_final: 0.7807 (m-80) REVERT: C 350 MET cc_start: 0.6854 (tpt) cc_final: 0.6530 (mmm) REVERT: C 391 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7372 (t80) REVERT: C 394 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.7341 (t-100) REVERT: C 444 PHE cc_start: 0.8171 (m-10) cc_final: 0.7362 (m-10) REVERT: C 495 GLU cc_start: 0.7193 (tp30) cc_final: 0.6636 (tm-30) REVERT: D 126 MET cc_start: 0.7562 (ttp) cc_final: 0.7338 (ttm) REVERT: D 142 ASP cc_start: 0.7261 (m-30) cc_final: 0.7056 (t0) REVERT: D 224 LEU cc_start: 0.8752 (mm) cc_final: 0.8460 (mm) REVERT: D 247 LEU cc_start: 0.9108 (mm) cc_final: 0.8496 (tt) REVERT: D 300 ASN cc_start: 0.6964 (t0) cc_final: 0.6416 (t0) REVERT: D 408 GLN cc_start: 0.8361 (mt0) cc_final: 0.7786 (mm110) REVERT: D 419 ARG cc_start: 0.5561 (ptt-90) cc_final: 0.4596 (ptm160) REVERT: D 453 PHE cc_start: 0.7397 (t80) cc_final: 0.7186 (t80) REVERT: D 473 TRP cc_start: 0.7994 (t-100) cc_final: 0.7710 (t-100) outliers start: 92 outliers final: 66 residues processed: 324 average time/residue: 0.2149 time to fit residues: 104.2543 Evaluate side-chains 330 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 254 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 119 HIS B 217 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN C 119 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13120 Z= 0.187 Angle : 0.671 10.797 17864 Z= 0.305 Chirality : 0.040 0.204 1984 Planarity : 0.004 0.044 2108 Dihedral : 7.063 52.917 2316 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.65 % Allowed : 27.01 % Favored : 67.34 % 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: -0.36 (0.22), residues: 1460 helix: 0.61 (0.16), residues: 1084 sheet: None (None), residues: 0 loop : -2.69 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 478 HIS 0.003 0.001 HIS D 217 PHE 0.013 0.001 PHE A 444 TYR 0.020 0.001 TYR B 182 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 264 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8492 (mt0) cc_final: 0.8044 (mp10) REVERT: A 115 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.6628 (mpm) REVERT: A 122 THR cc_start: 0.8717 (m) cc_final: 0.8437 (m) REVERT: A 223 GLN cc_start: 0.6971 (mt0) cc_final: 0.6324 (tm-30) REVERT: A 341 LEU cc_start: 0.8012 (tp) cc_final: 0.7735 (tp) REVERT: A 444 PHE cc_start: 0.8294 (m-10) cc_final: 0.8055 (m-10) REVERT: B 173 MET cc_start: 0.9304 (ppp) cc_final: 0.8966 (ppp) REVERT: B 224 LEU cc_start: 0.8697 (mm) cc_final: 0.8196 (mm) REVERT: B 237 VAL cc_start: 0.8996 (m) cc_final: 0.8740 (p) REVERT: B 247 LEU cc_start: 0.9181 (mm) cc_final: 0.8549 (tt) REVERT: B 281 ILE cc_start: 0.8464 (mm) cc_final: 0.7959 (tp) REVERT: B 283 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8337 (mmt90) REVERT: B 300 ASN cc_start: 0.7223 (m-40) cc_final: 0.6536 (t0) REVERT: B 350 MET cc_start: 0.7962 (mmm) cc_final: 0.7662 (tpp) REVERT: B 414 LEU cc_start: 0.8451 (mp) cc_final: 0.8093 (tp) REVERT: B 419 ARG cc_start: 0.5487 (ptt-90) cc_final: 0.4051 (ptm160) REVERT: B 473 TRP cc_start: 0.7975 (t-100) cc_final: 0.6751 (m-90) REVERT: B 492 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: B 495 GLU cc_start: 0.4833 (OUTLIER) cc_final: 0.4120 (mp0) REVERT: C 115 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.6583 (mpm) REVERT: C 221 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7561 (tt0) REVERT: C 286 TYR cc_start: 0.7984 (m-10) cc_final: 0.7708 (m-80) REVERT: C 391 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7263 (t80) REVERT: C 495 GLU cc_start: 0.7130 (tp30) cc_final: 0.6351 (tp30) REVERT: D 142 ASP cc_start: 0.7208 (m-30) cc_final: 0.6983 (t0) REVERT: D 173 MET cc_start: 0.8842 (ptt) cc_final: 0.8614 (ptt) REVERT: D 207 HIS cc_start: 0.8908 (t-90) cc_final: 0.8560 (t-90) REVERT: D 224 LEU cc_start: 0.8704 (mm) cc_final: 0.8388 (mm) REVERT: D 247 LEU cc_start: 0.9062 (mm) cc_final: 0.8479 (tt) REVERT: D 300 ASN cc_start: 0.6746 (t0) cc_final: 0.6227 (t0) REVERT: D 394 TRP cc_start: 0.7271 (t-100) cc_final: 0.6972 (t-100) REVERT: D 408 GLN cc_start: 0.8307 (mt0) cc_final: 0.7744 (mm110) REVERT: D 419 ARG cc_start: 0.5461 (ptt-90) cc_final: 0.4402 (ptm160) REVERT: D 473 TRP cc_start: 0.8022 (t-100) cc_final: 0.7724 (t-100) REVERT: D 495 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.4859 (mp0) outliers start: 73 outliers final: 52 residues processed: 317 average time/residue: 0.2155 time to fit residues: 102.5367 Evaluate side-chains 314 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS B 217 HIS B 236 GLN B 303 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13120 Z= 0.174 Angle : 0.669 11.148 17864 Z= 0.301 Chirality : 0.040 0.172 1984 Planarity : 0.004 0.045 2108 Dihedral : 6.930 59.895 2316 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.19 % Allowed : 27.48 % Favored : 67.34 % 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: -0.23 (0.22), residues: 1460 helix: 0.78 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.75 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 478 HIS 0.005 0.001 HIS D 360 PHE 0.025 0.001 PHE C 444 TYR 0.020 0.001 TYR B 182 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 271 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8477 (mt0) cc_final: 0.8057 (mp10) REVERT: A 115 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.6628 (mpm) REVERT: A 122 THR cc_start: 0.8696 (m) cc_final: 0.8426 (m) REVERT: A 223 GLN cc_start: 0.6961 (mt0) cc_final: 0.6454 (tm-30) REVERT: A 341 LEU cc_start: 0.7937 (tp) cc_final: 0.7480 (tp) REVERT: A 375 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7782 (mtt-85) REVERT: A 444 PHE cc_start: 0.8281 (m-10) cc_final: 0.7732 (m-10) REVERT: B 173 MET cc_start: 0.9322 (ppp) cc_final: 0.8945 (ppp) REVERT: B 177 THR cc_start: 0.9150 (t) cc_final: 0.8868 (t) REVERT: B 224 LEU cc_start: 0.8702 (mm) cc_final: 0.8187 (mm) REVERT: B 247 LEU cc_start: 0.9172 (mm) cc_final: 0.8562 (tt) REVERT: B 281 ILE cc_start: 0.8436 (mm) cc_final: 0.7880 (tp) REVERT: B 300 ASN cc_start: 0.7214 (m-40) cc_final: 0.6525 (t0) REVERT: B 350 MET cc_start: 0.7933 (mmm) cc_final: 0.7612 (tpp) REVERT: B 376 MET cc_start: 0.7314 (ttp) cc_final: 0.6955 (tpp) REVERT: B 394 TRP cc_start: 0.7100 (t-100) cc_final: 0.6719 (t-100) REVERT: B 414 LEU cc_start: 0.8508 (mp) cc_final: 0.8092 (tp) REVERT: B 419 ARG cc_start: 0.5471 (ptt-90) cc_final: 0.3999 (ptm160) REVERT: B 449 MET cc_start: 0.6186 (ttt) cc_final: 0.5493 (tpt) REVERT: B 473 TRP cc_start: 0.7986 (t-100) cc_final: 0.6805 (m-90) REVERT: B 492 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: B 495 GLU cc_start: 0.4926 (OUTLIER) cc_final: 0.4222 (mp0) REVERT: C 115 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.6597 (mpm) REVERT: C 221 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7575 (tt0) REVERT: C 286 TYR cc_start: 0.7981 (m-10) cc_final: 0.7740 (m-80) REVERT: C 391 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7172 (t80) REVERT: C 459 MET cc_start: 0.5232 (ttm) cc_final: 0.4994 (ttt) REVERT: D 142 ASP cc_start: 0.7216 (m-30) cc_final: 0.6978 (t0) REVERT: D 173 MET cc_start: 0.8816 (ptt) cc_final: 0.8555 (ptt) REVERT: D 207 HIS cc_start: 0.8860 (t-90) cc_final: 0.8569 (t-90) REVERT: D 224 LEU cc_start: 0.8706 (mm) cc_final: 0.8363 (mm) REVERT: D 247 LEU cc_start: 0.9081 (mm) cc_final: 0.8507 (tt) REVERT: D 300 ASN cc_start: 0.6782 (t0) cc_final: 0.6263 (t0) REVERT: D 394 TRP cc_start: 0.7203 (t-100) cc_final: 0.6936 (t-100) REVERT: D 408 GLN cc_start: 0.8351 (mt0) cc_final: 0.7735 (mm110) REVERT: D 419 ARG cc_start: 0.5443 (ptt-90) cc_final: 0.4361 (ptm160) REVERT: D 473 TRP cc_start: 0.7926 (t-100) cc_final: 0.6736 (m-90) REVERT: D 495 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4778 (mp0) outliers start: 67 outliers final: 50 residues processed: 318 average time/residue: 0.2140 time to fit residues: 101.9543 Evaluate side-chains 314 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 0.0040 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 119 HIS B 125 HIS B 217 HIS B 236 GLN B 303 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13120 Z= 0.214 Angle : 0.696 11.559 17864 Z= 0.317 Chirality : 0.041 0.156 1984 Planarity : 0.004 0.044 2108 Dihedral : 6.890 58.399 2316 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.57 % Allowed : 28.02 % Favored : 66.41 % 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: -0.24 (0.22), residues: 1460 helix: 0.73 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 478 HIS 0.005 0.001 HIS A 399 PHE 0.020 0.001 PHE C 444 TYR 0.020 0.001 TYR B 182 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 266 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8518 (mt0) cc_final: 0.8097 (mp10) REVERT: A 115 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.6639 (mpm) REVERT: A 122 THR cc_start: 0.8710 (m) cc_final: 0.8434 (m) REVERT: A 223 GLN cc_start: 0.6984 (mt0) cc_final: 0.6411 (tm-30) REVERT: A 341 LEU cc_start: 0.7818 (tp) cc_final: 0.7398 (tp) REVERT: B 173 MET cc_start: 0.9314 (ppp) cc_final: 0.8959 (ppp) REVERT: B 177 THR cc_start: 0.9127 (t) cc_final: 0.8860 (t) REVERT: B 224 LEU cc_start: 0.8745 (mm) cc_final: 0.8232 (mm) REVERT: B 247 LEU cc_start: 0.9178 (mm) cc_final: 0.8555 (tt) REVERT: B 281 ILE cc_start: 0.8511 (mm) cc_final: 0.7890 (tp) REVERT: B 300 ASN cc_start: 0.7251 (m-40) cc_final: 0.6540 (t0) REVERT: B 350 MET cc_start: 0.7917 (mmm) cc_final: 0.7573 (tpp) REVERT: B 376 MET cc_start: 0.7368 (ttp) cc_final: 0.6765 (tmm) REVERT: B 394 TRP cc_start: 0.7159 (t-100) cc_final: 0.6815 (t-100) REVERT: B 414 LEU cc_start: 0.8554 (mp) cc_final: 0.8122 (tp) REVERT: B 419 ARG cc_start: 0.5505 (ptt-90) cc_final: 0.4011 (ptm160) REVERT: B 473 TRP cc_start: 0.7995 (t-100) cc_final: 0.6799 (m-90) REVERT: B 492 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: B 495 GLU cc_start: 0.4983 (OUTLIER) cc_final: 0.4286 (mp0) REVERT: C 115 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.6702 (mpm) REVERT: C 286 TYR cc_start: 0.8048 (m-10) cc_final: 0.7792 (m-80) REVERT: C 391 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7281 (t80) REVERT: C 394 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.6789 (t-100) REVERT: D 142 ASP cc_start: 0.7264 (m-30) cc_final: 0.7022 (t0) REVERT: D 207 HIS cc_start: 0.8922 (t-90) cc_final: 0.8555 (t-90) REVERT: D 224 LEU cc_start: 0.8774 (mm) cc_final: 0.8424 (mm) REVERT: D 247 LEU cc_start: 0.9079 (mm) cc_final: 0.8511 (tt) REVERT: D 300 ASN cc_start: 0.6860 (t0) cc_final: 0.6300 (t0) REVERT: D 394 TRP cc_start: 0.7205 (t-100) cc_final: 0.6996 (t-100) REVERT: D 408 GLN cc_start: 0.8355 (mt0) cc_final: 0.7733 (mm110) REVERT: D 419 ARG cc_start: 0.5475 (ptt-90) cc_final: 0.4279 (ptm160) REVERT: D 473 TRP cc_start: 0.7920 (t-100) cc_final: 0.6726 (m-90) REVERT: D 495 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.4753 (mp0) outliers start: 72 outliers final: 54 residues processed: 319 average time/residue: 0.2000 time to fit residues: 95.9245 Evaluate side-chains 315 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 254 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 119 HIS B 125 HIS B 217 HIS B 303 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13120 Z= 0.191 Angle : 0.695 11.175 17864 Z= 0.313 Chirality : 0.040 0.149 1984 Planarity : 0.004 0.045 2108 Dihedral : 6.768 53.043 2316 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.57 % Allowed : 29.10 % Favored : 66.33 % 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: -0.21 (0.22), residues: 1460 helix: 0.74 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 478 HIS 0.004 0.001 HIS D 360 PHE 0.020 0.001 PHE D 440 TYR 0.020 0.001 TYR B 182 ARG 0.004 0.000 ARG A 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8522 (mt0) cc_final: 0.8100 (mp10) REVERT: A 115 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6722 (mpm) REVERT: A 122 THR cc_start: 0.8690 (m) cc_final: 0.8411 (m) REVERT: A 223 GLN cc_start: 0.6977 (mt0) cc_final: 0.6429 (tm-30) REVERT: A 341 LEU cc_start: 0.7773 (tp) cc_final: 0.7378 (tp) REVERT: A 375 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7762 (mtt-85) REVERT: B 173 MET cc_start: 0.9317 (ppp) cc_final: 0.9030 (ppp) REVERT: B 177 THR cc_start: 0.9073 (t) cc_final: 0.8782 (t) REVERT: B 224 LEU cc_start: 0.8715 (mm) cc_final: 0.8194 (mm) REVERT: B 247 LEU cc_start: 0.9173 (mm) cc_final: 0.8573 (tt) REVERT: B 281 ILE cc_start: 0.8511 (mm) cc_final: 0.7905 (tp) REVERT: B 300 ASN cc_start: 0.7240 (m-40) cc_final: 0.6499 (t0) REVERT: B 350 MET cc_start: 0.7961 (mmm) cc_final: 0.7686 (tpp) REVERT: B 360 HIS cc_start: 0.7852 (t-90) cc_final: 0.7599 (t-170) REVERT: B 376 MET cc_start: 0.7312 (ttp) cc_final: 0.6746 (tmm) REVERT: B 394 TRP cc_start: 0.7124 (t-100) cc_final: 0.6759 (t-100) REVERT: B 414 LEU cc_start: 0.8516 (mp) cc_final: 0.8071 (tp) REVERT: B 419 ARG cc_start: 0.5457 (ptt-90) cc_final: 0.3942 (ptm160) REVERT: B 473 TRP cc_start: 0.7958 (t-100) cc_final: 0.6786 (m-90) REVERT: B 492 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: B 495 GLU cc_start: 0.4939 (OUTLIER) cc_final: 0.4241 (mp0) REVERT: C 115 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.6628 (mpm) REVERT: C 223 GLN cc_start: 0.6892 (mt0) cc_final: 0.6110 (pp30) REVERT: C 286 TYR cc_start: 0.7979 (m-10) cc_final: 0.7754 (m-80) REVERT: C 391 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7181 (t80) REVERT: D 142 ASP cc_start: 0.7222 (m-30) cc_final: 0.6989 (t0) REVERT: D 203 LEU cc_start: 0.8839 (mt) cc_final: 0.8312 (tp) REVERT: D 207 HIS cc_start: 0.8899 (t-90) cc_final: 0.8656 (t-90) REVERT: D 224 LEU cc_start: 0.8793 (mm) cc_final: 0.8438 (mm) REVERT: D 247 LEU cc_start: 0.9114 (mm) cc_final: 0.8533 (tt) REVERT: D 300 ASN cc_start: 0.6735 (t0) cc_final: 0.6213 (t0) REVERT: D 408 GLN cc_start: 0.8325 (mt0) cc_final: 0.7713 (mm110) REVERT: D 419 ARG cc_start: 0.5384 (ptt-90) cc_final: 0.4183 (ptm160) REVERT: D 473 TRP cc_start: 0.7911 (t-100) cc_final: 0.6701 (m-90) REVERT: D 495 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.4804 (mp0) outliers start: 59 outliers final: 47 residues processed: 304 average time/residue: 0.2146 time to fit residues: 97.7088 Evaluate side-chains 304 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 495 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 383 ASN B 217 HIS B 303 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS D 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109672 restraints weight = 21648.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112305 restraints weight = 12116.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114063 restraints weight = 8430.845| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13120 Z= 0.174 Angle : 0.691 10.836 17864 Z= 0.311 Chirality : 0.039 0.145 1984 Planarity : 0.004 0.046 2108 Dihedral : 6.721 52.577 2316 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.72 % Allowed : 29.26 % Favored : 66.02 % 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: -0.15 (0.22), residues: 1460 helix: 0.73 (0.16), residues: 1084 sheet: None (None), residues: 0 loop : -2.52 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 478 HIS 0.005 0.001 HIS D 360 PHE 0.014 0.001 PHE C 444 TYR 0.020 0.001 TYR B 182 ARG 0.003 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2729.20 seconds wall clock time: 50 minutes 23.32 seconds (3023.32 seconds total)