Starting phenix.real_space_refine on Sat Jul 20 23:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/07_2024/7l49_23158_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/07_2024/7l49_23158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/07_2024/7l49_23158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/07_2024/7l49_23158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/07_2024/7l49_23158_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l49_23158/07_2024/7l49_23158_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 190 5.49 5 S 37 5.16 5 C 7186 2.51 5 N 2218 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B ARG 490": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 599 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC%5*END:plan2': 1, ' DC%5*END:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2877 Classifications: {'RNA': 135} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 14, 'rna3p': 120} Chain breaks: 2 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3858 SG CYS A 478 7.021 61.788 44.308 1.00 37.58 S ATOM 4048 SG CYS A 500 10.720 61.502 41.558 1.00 40.36 S ATOM 364 SG CYS A 50 53.252 98.716 77.958 1.00 42.34 S ATOM 502 SG CYS A 69 57.157 99.263 78.476 1.00 31.65 S ATOM 527 SG CYS A 72 55.385 96.180 79.439 1.00 31.06 S ATOM 8043 SG CYS B 478 59.449 58.052 9.211 1.00 58.65 S ATOM 8229 SG CYS B 500 56.592 59.678 11.519 1.00 65.09 S Time building chain proxies: 7.58, per 1000 atoms: 0.61 Number of scatterers: 12414 At special positions: 0 Unit cell: (102.9, 121.8, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 37 16.00 P 190 15.00 O 2779 8.00 N 2218 7.00 C 7186 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: 5.85 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 478 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 500 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 46.0% alpha, 10.5% beta 59 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 Processing helix chain 'A' and resid 52 through 58 removed outlier: 4.153A pdb=" N VAL A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 58' Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.678A pdb=" N ARG A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.931A pdb=" N TYR A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.575A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.644A pdb=" N ASN A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.901A pdb=" N GLU A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 350 through 367 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 382 through 414 removed outlier: 3.707A pdb=" N THR A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 518 removed outlier: 3.597A pdb=" N ALA A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 41 removed outlier: 3.557A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.968A pdb=" N VAL B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.747A pdb=" N ALA B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.626A pdb=" N TYR B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.664A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.958A pdb=" N PHE B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.569A pdb=" N SER B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 4.198A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.612A pdb=" N GLU B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.991A pdb=" N LYS B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 414 Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 444 through 459 removed outlier: 3.866A pdb=" N TYR B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.581A pdb=" N LYS B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.632A pdb=" N ALA B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.340A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER A 251 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 16 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP A 302 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 287 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.532A pdb=" N VAL A 334 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 416 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 321 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 325 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 422 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL A 327 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY A 417 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ARG A 464 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 419 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 466 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET A 421 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.713A pdb=" N GLU A 507 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 7.396A pdb=" N SER B 251 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 253 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 255 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TRP B 302 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 6.532A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 499 376 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3322 1.34 - 1.47: 4068 1.47 - 1.59: 5248 1.59 - 1.71: 365 1.71 - 1.84: 51 Bond restraints: 13054 Sorted by residual: bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" N ILE B 385 " pdb=" CA ILE B 385 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N CYS B 50 " pdb=" CA CYS B 50 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.65e+00 bond pdb=" N LEU B 382 " pdb=" CA LEU B 382 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.42e-02 4.96e+03 6.96e+00 bond pdb=" N ARG A 438 " pdb=" CA ARG A 438 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.42e-02 4.96e+03 6.94e+00 ... (remaining 13049 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.72: 866 104.72 - 112.10: 6477 112.10 - 119.48: 4756 119.48 - 126.85: 5785 126.85 - 134.23: 571 Bond angle restraints: 18455 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CA PRO B 384 " pdb=" C PRO B 384 " ideal model delta sigma weight residual 113.40 121.56 -8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" C GLU B 65 " pdb=" N ARG B 66 " pdb=" CA ARG B 66 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C4' G E 190 " pdb=" C3' G E 190 " pdb=" O3' G E 190 " ideal model delta sigma weight residual 109.40 117.19 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" C CYS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" CA TRP B 223 " pdb=" CB TRP B 223 " pdb=" CG TRP B 223 " ideal model delta sigma weight residual 113.60 122.51 -8.91 1.90e+00 2.77e-01 2.20e+01 ... (remaining 18450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 7306 35.71 - 71.42: 590 71.42 - 107.13: 41 107.13 - 142.84: 2 142.84 - 178.54: 2 Dihedral angle restraints: 7941 sinusoidal: 4874 harmonic: 3067 Sorted by residual: dihedral pdb=" O4' U E 92 " pdb=" C1' U E 92 " pdb=" N1 U E 92 " pdb=" C2 U E 92 " ideal model delta sinusoidal sigma weight residual 232.00 53.46 178.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C E 77 " pdb=" C1' C E 77 " pdb=" N1 C E 77 " pdb=" C2 C E 77 " ideal model delta sinusoidal sigma weight residual 232.00 56.83 175.17 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U E 110 " pdb=" C1' U E 110 " pdb=" N1 U E 110 " pdb=" C2 U E 110 " ideal model delta sinusoidal sigma weight residual -160.00 -61.24 -98.76 1 1.50e+01 4.44e-03 4.92e+01 ... (remaining 7938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1904 0.093 - 0.186: 193 0.186 - 0.279: 16 0.279 - 0.372: 5 0.372 - 0.465: 1 Chirality restraints: 2119 Sorted by residual: chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C3' G E 190 " pdb=" C4' G E 190 " pdb=" O3' G E 190 " pdb=" C2' G E 190 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB THR A 389 " pdb=" CA THR A 389 " pdb=" OG1 THR A 389 " pdb=" CG2 THR A 389 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2116 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 42 " -0.031 2.00e-02 2.50e+03 2.42e-02 1.61e+01 pdb=" N9 DA C 42 " 0.064 2.00e-02 2.50e+03 pdb=" C8 DA C 42 " -0.033 2.00e-02 2.50e+03 pdb=" N7 DA C 42 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA C 42 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA C 42 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA C 42 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA C 42 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 197 " 0.024 2.00e-02 2.50e+03 2.31e-02 1.20e+01 pdb=" N1 U E 197 " -0.055 2.00e-02 2.50e+03 pdb=" C2 U E 197 " 0.031 2.00e-02 2.50e+03 pdb=" O2 U E 197 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U E 197 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U E 197 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U E 197 " 0.001 2.00e-02 2.50e+03 pdb=" C5 U E 197 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U E 197 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 123 " 0.026 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" N1 C E 123 " -0.056 2.00e-02 2.50e+03 pdb=" C2 C E 123 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C E 123 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C E 123 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C E 123 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C E 123 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C E 123 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C E 123 " 0.005 2.00e-02 2.50e+03 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1453 2.76 - 3.29: 10809 3.29 - 3.83: 22411 3.83 - 4.36: 27377 4.36 - 4.90: 41752 Nonbonded interactions: 103802 Sorted by model distance: nonbonded pdb=" N3 C E 22 " pdb=" N1 G E 71 " model vdw 2.220 2.600 nonbonded pdb=" OG1 THR A 9 " pdb=" O2' A E 203 " model vdw 2.282 2.440 nonbonded pdb=" N4 C E 22 " pdb=" O6 G E 71 " model vdw 2.283 2.520 nonbonded pdb=" O2 C E 87 " pdb=" O2' A E 129 " model vdw 2.291 2.440 nonbonded pdb=" O PHE B 341 " pdb=" OH TYR B 511 " model vdw 2.296 2.440 ... (remaining 103797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 525 or resid 601 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 41.150 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.005 0.063 13054 Z= 0.308 Angle : 0.948 12.650 18455 Z= 0.552 Chirality : 0.059 0.465 2119 Planarity : 0.007 0.065 1666 Dihedral : 21.426 178.545 5951 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: -3.90 (0.21), residues: 1037 helix: -2.17 (0.19), residues: 444 sheet: -2.23 (0.37), residues: 167 loop : -3.07 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 223 HIS 0.014 0.001 HIS A 53 PHE 0.026 0.002 PHE B 220 TYR 0.021 0.002 TYR B 113 ARG 0.013 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 232 TYR cc_start: 0.6934 (m-80) cc_final: 0.6706 (m-10) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3406 time to fit residues: 57.6730 Evaluate side-chains 87 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 380 ASN A 493 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13054 Z= 0.295 Angle : 0.613 8.213 18455 Z= 0.327 Chirality : 0.039 0.208 2119 Planarity : 0.005 0.050 1666 Dihedral : 21.932 174.946 3799 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.78 % Allowed : 11.36 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.24), residues: 1037 helix: -0.45 (0.23), residues: 458 sheet: -1.51 (0.41), residues: 155 loop : -2.72 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 302 HIS 0.008 0.001 HIS A 53 PHE 0.020 0.002 PHE A 205 TYR 0.016 0.002 TYR A 82 ARG 0.006 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.158 Fit side-chains REVERT: B 343 ARG cc_start: 0.7516 (ptp-170) cc_final: 0.7208 (ptp-170) REVERT: B 511 TYR cc_start: 0.7962 (t80) cc_final: 0.7732 (t80) outliers start: 7 outliers final: 4 residues processed: 114 average time/residue: 0.3492 time to fit residues: 54.5819 Evaluate side-chains 99 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13054 Z= 0.313 Angle : 0.589 7.048 18455 Z= 0.316 Chirality : 0.040 0.188 2119 Planarity : 0.004 0.053 1666 Dihedral : 22.077 177.316 3799 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.23 % Allowed : 13.59 % Favored : 84.19 % 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: -1.63 (0.25), residues: 1037 helix: 0.31 (0.24), residues: 460 sheet: -1.27 (0.43), residues: 150 loop : -2.60 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 265 HIS 0.007 0.001 HIS A 53 PHE 0.025 0.002 PHE B 205 TYR 0.020 0.002 TYR A 82 ARG 0.006 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.128 Fit side-chains REVERT: A 425 GLU cc_start: 0.7347 (tp30) cc_final: 0.6685 (pp20) REVERT: B 98 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8003 (tt) REVERT: B 153 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8132 (p90) outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 0.2925 time to fit residues: 46.0102 Evaluate side-chains 99 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 497 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13054 Z= 0.349 Angle : 0.602 7.538 18455 Z= 0.320 Chirality : 0.041 0.193 2119 Planarity : 0.004 0.051 1666 Dihedral : 22.054 176.436 3799 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.67 % Allowed : 15.59 % Favored : 81.74 % 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: -1.36 (0.26), residues: 1037 helix: 0.54 (0.24), residues: 461 sheet: -1.18 (0.44), residues: 151 loop : -2.46 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 265 HIS 0.007 0.001 HIS A 53 PHE 0.019 0.002 PHE A 214 TYR 0.020 0.002 TYR A 82 ARG 0.004 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.128 Fit side-chains REVERT: A 425 GLU cc_start: 0.7562 (tp30) cc_final: 0.6859 (pp20) REVERT: A 491 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7481 (mtmm) REVERT: B 98 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8080 (tt) REVERT: B 153 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7963 (p90) outliers start: 24 outliers final: 16 residues processed: 109 average time/residue: 0.2921 time to fit residues: 44.1708 Evaluate side-chains 101 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13054 Z= 0.314 Angle : 0.574 7.348 18455 Z= 0.306 Chirality : 0.040 0.185 2119 Planarity : 0.004 0.048 1666 Dihedral : 22.058 177.114 3799 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.67 % Allowed : 16.70 % Favored : 80.62 % 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: -1.18 (0.26), residues: 1037 helix: 0.72 (0.24), residues: 462 sheet: -1.16 (0.44), residues: 151 loop : -2.37 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 265 HIS 0.005 0.001 HIS A 53 PHE 0.017 0.002 PHE A 214 TYR 0.020 0.002 TYR A 82 ARG 0.005 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.173 Fit side-chains REVERT: A 425 GLU cc_start: 0.7579 (tp30) cc_final: 0.6957 (pp20) REVERT: A 491 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7468 (mtmm) REVERT: B 98 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 153 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7927 (p90) outliers start: 24 outliers final: 15 residues processed: 106 average time/residue: 0.2818 time to fit residues: 41.8519 Evaluate side-chains 98 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13054 Z= 0.200 Angle : 0.513 7.160 18455 Z= 0.274 Chirality : 0.036 0.159 2119 Planarity : 0.003 0.040 1666 Dihedral : 21.926 179.508 3799 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.12 % Allowed : 17.04 % Favored : 80.85 % 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: -0.90 (0.26), residues: 1037 helix: 1.05 (0.24), residues: 460 sheet: -1.11 (0.44), residues: 150 loop : -2.30 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 443 HIS 0.003 0.001 HIS B 353 PHE 0.013 0.001 PHE A 205 TYR 0.016 0.001 TYR A 82 ARG 0.004 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.188 Fit side-chains REVERT: A 425 GLU cc_start: 0.7418 (tp30) cc_final: 0.6865 (pt0) REVERT: A 491 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7377 (mtmm) REVERT: B 98 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8049 (tt) REVERT: B 153 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7728 (p90) REVERT: B 383 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7693 (mmtt) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 0.3016 time to fit residues: 43.7673 Evaluate side-chains 96 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN B 63 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13054 Z= 0.331 Angle : 0.580 7.393 18455 Z= 0.308 Chirality : 0.040 0.189 2119 Planarity : 0.004 0.046 1666 Dihedral : 22.058 177.298 3799 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.45 % Allowed : 17.82 % Favored : 79.73 % 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: -0.98 (0.26), residues: 1037 helix: 0.94 (0.24), residues: 462 sheet: -1.08 (0.44), residues: 151 loop : -2.33 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 265 HIS 0.006 0.001 HIS A 53 PHE 0.017 0.002 PHE A 214 TYR 0.020 0.002 TYR A 82 ARG 0.004 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.268 Fit side-chains REVERT: A 425 GLU cc_start: 0.7594 (tp30) cc_final: 0.6895 (pp20) REVERT: A 491 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7405 (mtmm) REVERT: B 98 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8156 (tt) REVERT: B 153 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8015 (p90) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.2925 time to fit residues: 42.5908 Evaluate side-chains 100 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 chunk 108 optimal weight: 7.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13054 Z= 0.345 Angle : 0.598 9.043 18455 Z= 0.315 Chirality : 0.040 0.194 2119 Planarity : 0.004 0.046 1666 Dihedral : 22.090 176.939 3799 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.56 % Allowed : 18.37 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1037 helix: 0.89 (0.24), residues: 460 sheet: -1.05 (0.45), residues: 144 loop : -2.37 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 265 HIS 0.005 0.001 HIS A 53 PHE 0.017 0.002 PHE A 214 TYR 0.021 0.002 TYR A 82 ARG 0.004 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.064 Fit side-chains REVERT: A 425 GLU cc_start: 0.7551 (tp30) cc_final: 0.6845 (pp20) REVERT: A 483 ASN cc_start: 0.8319 (t0) cc_final: 0.7982 (t0) REVERT: A 491 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7558 (mtmm) REVERT: B 98 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 153 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8033 (p90) outliers start: 23 outliers final: 17 residues processed: 108 average time/residue: 0.2893 time to fit residues: 43.5157 Evaluate side-chains 103 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13054 Z= 0.338 Angle : 0.594 8.672 18455 Z= 0.313 Chirality : 0.040 0.191 2119 Planarity : 0.004 0.046 1666 Dihedral : 22.106 177.252 3799 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.23 % Allowed : 18.82 % Favored : 78.95 % 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: -1.07 (0.26), residues: 1037 helix: 0.87 (0.24), residues: 461 sheet: -1.12 (0.43), residues: 149 loop : -2.38 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 265 HIS 0.004 0.001 HIS A 53 PHE 0.023 0.002 PHE B 487 TYR 0.020 0.002 TYR A 82 ARG 0.004 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.124 Fit side-chains REVERT: A 425 GLU cc_start: 0.7585 (tp30) cc_final: 0.6836 (pp20) REVERT: A 491 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7580 (mtmm) REVERT: B 98 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 153 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8022 (p90) outliers start: 20 outliers final: 18 residues processed: 103 average time/residue: 0.3030 time to fit residues: 43.3555 Evaluate side-chains 102 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13054 Z= 0.188 Angle : 0.522 9.202 18455 Z= 0.275 Chirality : 0.037 0.204 2119 Planarity : 0.004 0.040 1666 Dihedral : 21.925 179.819 3799 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.00 % Allowed : 19.49 % Favored : 78.51 % 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: -0.81 (0.26), residues: 1037 helix: 1.15 (0.24), residues: 462 sheet: -1.07 (0.43), residues: 148 loop : -2.30 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.003 0.001 HIS B 353 PHE 0.015 0.001 PHE B 454 TYR 0.017 0.001 TYR A 82 ARG 0.004 0.000 ARG B 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.124 Fit side-chains REVERT: A 425 GLU cc_start: 0.7475 (tp30) cc_final: 0.6874 (pt0) REVERT: A 491 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7359 (mtmm) REVERT: B 98 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 153 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7678 (p90) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.2930 time to fit residues: 44.5916 Evaluate side-chains 104 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.0770 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.180716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135506 restraints weight = 13663.442| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.65 r_work: 0.3264 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13054 Z= 0.164 Angle : 0.499 10.513 18455 Z= 0.264 Chirality : 0.036 0.214 2119 Planarity : 0.003 0.037 1666 Dihedral : 21.728 178.312 3799 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.00 % Allowed : 19.71 % Favored : 78.29 % 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: -0.53 (0.27), residues: 1037 helix: 1.38 (0.24), residues: 462 sheet: -0.72 (0.45), residues: 140 loop : -2.23 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.004 0.001 HIS B 353 PHE 0.012 0.001 PHE A 205 TYR 0.015 0.001 TYR B 113 ARG 0.004 0.000 ARG B 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.97 seconds wall clock time: 42 minutes 15.82 seconds (2535.82 seconds total)