Starting phenix.real_space_refine on Wed Jan 17 22:23:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8b_31796/01_2024/7v8b_31796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8b_31796/01_2024/7v8b_31796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8b_31796/01_2024/7v8b_31796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8b_31796/01_2024/7v8b_31796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8b_31796/01_2024/7v8b_31796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8b_31796/01_2024/7v8b_31796.pdb" } resolution = 3.2 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= -0.001 sd= 0.032 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 37 5.16 5 C 4242 2.51 5 N 1088 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6650 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.11, per 1000 atoms: 0.62 Number of scatterers: 6650 At special positions: 0 Unit cell: (79.2, 105.6, 125.4, 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 37 16.00 O 1283 8.00 N 1088 7.00 C 4242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.02 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 103 " " NAG E 1 " - " ASN F 322 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 432 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 55.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.667A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.835A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.987A pdb=" N TYR A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.797A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 59 through 80 removed outlier: 4.515A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.765A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.877A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.812A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'F' and resid 175 through 194 removed outlier: 4.361A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.513A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 231 removed outlier: 3.890A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.635A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.182A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.532A pdb=" N GLU F 312 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.956A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.645A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.509A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.757A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.790A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.560A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.785A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 4.468A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.950A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'F' and resid 347 through 350 281 hydrogen bonds defined for protein. 786 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: 1.68 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2109 1.34 - 1.46: 1732 1.46 - 1.58: 2933 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6832 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C1 NAG F2001 " pdb=" O5 NAG F2001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 ... (remaining 6827 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 217 106.71 - 113.52: 3649 113.52 - 120.34: 2565 120.34 - 127.15: 2755 127.15 - 133.97: 96 Bond angle restraints: 9282 Sorted by residual: angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 122.68 -8.28 2.30e+00 1.89e-01 1.30e+01 angle pdb=" CB ARG F 192 " pdb=" CG ARG F 192 " pdb=" CD ARG F 192 " ideal model delta sigma weight residual 111.30 118.38 -7.08 2.30e+00 1.89e-01 9.49e+00 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 120.75 -6.35 2.30e+00 1.89e-01 7.62e+00 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 108.79 112.66 -3.87 1.53e+00 4.27e-01 6.40e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 124.32 -8.02 3.50e+00 8.16e-02 5.25e+00 ... (remaining 9277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 3857 21.70 - 43.40: 304 43.40 - 65.10: 36 65.10 - 86.80: 15 86.80 - 108.49: 7 Dihedral angle restraints: 4219 sinusoidal: 1881 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASN F 432 " pdb=" C ASN F 432 " pdb=" N GLU F 433 " pdb=" CA GLU F 433 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 825 0.055 - 0.110: 164 0.110 - 0.164: 18 0.164 - 0.219: 2 0.219 - 0.274: 1 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1007 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 192 " -0.129 9.50e-02 1.11e+02 5.82e-02 2.64e+00 pdb=" NE ARG F 192 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 192 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 192 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 192 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 425 " -0.025 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO F 426 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 426 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 426 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 134 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO F 135 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 135 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 135 " -0.021 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2068 2.83 - 3.34: 6211 3.34 - 3.86: 10347 3.86 - 4.38: 11645 4.38 - 4.90: 20266 Nonbonded interactions: 50537 Sorted by model distance: nonbonded pdb=" OG SER A 349 " pdb=" O ARG A 452 " model vdw 2.308 2.440 nonbonded pdb=" O THR F 125 " pdb=" OG1 THR F 129 " model vdw 2.311 2.440 nonbonded pdb=" NH1 ARG F 177 " pdb=" O GLU F 495 " model vdw 2.340 2.520 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.357 2.520 nonbonded pdb=" NE1 TRP F 271 " pdb=" O SER F 502 " model vdw 2.380 2.520 ... (remaining 50532 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 8.350 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: 11.650 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.200 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6832 Z= 0.209 Angle : 0.586 8.282 9282 Z= 0.289 Chirality : 0.044 0.274 1010 Planarity : 0.004 0.058 1184 Dihedral : 15.613 108.494 2698 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.30), residues: 793 helix: 0.72 (0.28), residues: 369 sheet: 1.04 (0.80), residues: 47 loop : -1.38 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 477 HIS 0.006 0.001 HIS F 374 PHE 0.011 0.001 PHE F 603 TYR 0.012 0.001 TYR F 50 ARG 0.013 0.001 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.794 Fit side-chains REVERT: A 516 GLU cc_start: 0.6126 (tt0) cc_final: 0.5917 (tt0) REVERT: F 427 ASP cc_start: 0.7731 (p0) cc_final: 0.7337 (p0) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1849 time to fit residues: 15.3598 Evaluate side-chains 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 6832 Z= 0.435 Angle : 0.680 9.995 9282 Z= 0.349 Chirality : 0.047 0.247 1010 Planarity : 0.004 0.047 1184 Dihedral : 8.690 56.735 1158 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 0.71 % Allowed : 8.29 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 793 helix: 0.87 (0.28), residues: 371 sheet: 1.43 (0.81), residues: 44 loop : -1.52 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 477 HIS 0.005 0.002 HIS F 378 PHE 0.015 0.001 PHE F 523 TYR 0.016 0.002 TYR F 381 ARG 0.005 0.001 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.858 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.1955 time to fit residues: 13.5559 Evaluate side-chains 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6832 Z= 0.186 Angle : 0.545 9.594 9282 Z= 0.276 Chirality : 0.041 0.237 1010 Planarity : 0.003 0.034 1184 Dihedral : 7.311 56.182 1158 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 0.71 % Allowed : 10.71 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 793 helix: 1.13 (0.28), residues: 376 sheet: 1.45 (0.82), residues: 44 loop : -1.46 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.009 0.001 PHE F 523 TYR 0.012 0.001 TYR F 183 ARG 0.003 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.796 Fit side-chains REVERT: A 442 ASP cc_start: 0.7063 (m-30) cc_final: 0.6826 (m-30) outliers start: 5 outliers final: 0 residues processed: 51 average time/residue: 0.1891 time to fit residues: 13.5501 Evaluate side-chains 45 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6832 Z= 0.220 Angle : 0.541 9.689 9282 Z= 0.274 Chirality : 0.041 0.242 1010 Planarity : 0.003 0.031 1184 Dihedral : 6.804 55.968 1158 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.45 % Rotamer: Outliers : 1.29 % Allowed : 12.14 % Favored : 86.57 % 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: 0.09 (0.31), residues: 793 helix: 1.27 (0.29), residues: 376 sheet: 1.46 (0.83), residues: 44 loop : -1.44 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.010 0.001 PHE F 523 TYR 0.012 0.001 TYR F 183 ARG 0.002 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.761 Fit side-chains REVERT: A 442 ASP cc_start: 0.7129 (m-30) cc_final: 0.6884 (m-30) REVERT: F 584 LEU cc_start: 0.9011 (tp) cc_final: 0.8797 (tp) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.1877 time to fit residues: 14.6679 Evaluate side-chains 49 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6832 Z= 0.245 Angle : 0.551 9.770 9282 Z= 0.279 Chirality : 0.042 0.252 1010 Planarity : 0.003 0.030 1184 Dihedral : 6.743 56.530 1158 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 1.86 % Allowed : 13.00 % Favored : 85.14 % 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: 0.14 (0.31), residues: 793 helix: 1.34 (0.29), residues: 376 sheet: 1.42 (0.83), residues: 44 loop : -1.45 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE F 523 TYR 0.013 0.001 TYR F 183 ARG 0.002 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.740 Fit side-chains REVERT: A 442 ASP cc_start: 0.7171 (m-30) cc_final: 0.6904 (m-30) REVERT: F 427 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7343 (p0) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 0.1760 time to fit residues: 14.2154 Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6832 Z= 0.225 Angle : 0.556 9.737 9282 Z= 0.276 Chirality : 0.041 0.245 1010 Planarity : 0.003 0.029 1184 Dihedral : 6.751 59.263 1158 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 14.29 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.31), residues: 793 helix: 1.43 (0.29), residues: 372 sheet: 1.45 (0.84), residues: 44 loop : -1.48 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE F 523 TYR 0.013 0.001 TYR F 183 ARG 0.002 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.833 Fit side-chains REVERT: A 442 ASP cc_start: 0.7163 (m-30) cc_final: 0.6892 (m-30) REVERT: F 427 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7195 (p0) outliers start: 13 outliers final: 5 residues processed: 58 average time/residue: 0.1769 time to fit residues: 14.6363 Evaluate side-chains 50 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 427 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 6832 Z= 0.474 Angle : 0.698 9.895 9282 Z= 0.356 Chirality : 0.047 0.257 1010 Planarity : 0.004 0.033 1184 Dihedral : 6.906 55.488 1158 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 2.14 % Allowed : 15.00 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.30), residues: 793 helix: 1.06 (0.28), residues: 374 sheet: 1.44 (0.83), residues: 44 loop : -1.68 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 477 HIS 0.005 0.001 HIS A 519 PHE 0.021 0.002 PHE F 523 TYR 0.017 0.002 TYR A 453 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7401 (m-30) cc_final: 0.7108 (m-30) REVERT: F 190 MET cc_start: 0.8638 (tmm) cc_final: 0.8431 (tmm) REVERT: F 323 MET cc_start: 0.7315 (mtp) cc_final: 0.6987 (mtp) REVERT: F 376 MET cc_start: 0.8583 (mmt) cc_final: 0.8365 (mmt) REVERT: F 427 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7350 (p0) outliers start: 15 outliers final: 10 residues processed: 57 average time/residue: 0.1884 time to fit residues: 15.1037 Evaluate side-chains 56 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6832 Z= 0.196 Angle : 0.564 9.719 9282 Z= 0.282 Chirality : 0.042 0.244 1010 Planarity : 0.003 0.028 1184 Dihedral : 6.365 55.855 1158 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 2.00 % Allowed : 15.00 % Favored : 83.00 % 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: 0.04 (0.31), residues: 793 helix: 1.31 (0.29), residues: 372 sheet: 1.38 (0.83), residues: 44 loop : -1.53 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 603 TYR 0.014 0.001 TYR F 183 ARG 0.002 0.000 ARG F 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7126 (m-30) cc_final: 0.6839 (m-30) REVERT: F 190 MET cc_start: 0.8662 (tmm) cc_final: 0.8450 (tmm) REVERT: F 427 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7287 (p0) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.1671 time to fit residues: 13.4837 Evaluate side-chains 55 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6832 Z= 0.164 Angle : 0.542 9.710 9282 Z= 0.268 Chirality : 0.041 0.240 1010 Planarity : 0.003 0.030 1184 Dihedral : 6.022 55.519 1158 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 14.71 % Favored : 83.43 % 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: 0.18 (0.31), residues: 793 helix: 1.39 (0.29), residues: 375 sheet: 1.43 (0.85), residues: 44 loop : -1.42 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.011 0.001 PHE F 603 TYR 0.013 0.001 TYR F 183 ARG 0.001 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7147 (m-30) cc_final: 0.6863 (m-30) REVERT: F 376 MET cc_start: 0.8769 (tpp) cc_final: 0.8398 (mmt) REVERT: F 427 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7272 (p0) outliers start: 13 outliers final: 10 residues processed: 56 average time/residue: 0.1842 time to fit residues: 14.6012 Evaluate side-chains 55 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6832 Z= 0.167 Angle : 0.547 9.699 9282 Z= 0.271 Chirality : 0.041 0.240 1010 Planarity : 0.003 0.031 1184 Dihedral : 5.915 55.400 1158 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.45 % Rotamer: Outliers : 1.71 % Allowed : 15.57 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 793 helix: 1.44 (0.29), residues: 374 sheet: 1.47 (0.85), residues: 44 loop : -1.43 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.010 0.001 PHE F 603 TYR 0.013 0.001 TYR F 183 ARG 0.002 0.000 ARG F 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7175 (m-30) cc_final: 0.6904 (m-30) REVERT: F 427 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7269 (p0) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.1810 time to fit residues: 14.6176 Evaluate side-chains 56 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 442 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056949 restraints weight = 21545.913| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.33 r_work: 0.2913 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6832 Z= 0.135 Angle : 0.550 14.964 9282 Z= 0.261 Chirality : 0.040 0.236 1010 Planarity : 0.003 0.031 1184 Dihedral : 5.739 55.513 1158 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 1.57 % Allowed : 16.00 % Favored : 82.43 % 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: 0.28 (0.31), residues: 793 helix: 1.49 (0.29), residues: 374 sheet: 1.28 (0.84), residues: 46 loop : -1.39 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.010 0.001 PHE F 603 TYR 0.012 0.001 TYR F 183 ARG 0.001 0.000 ARG F 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.75 seconds wall clock time: 29 minutes 8.52 seconds (1748.52 seconds total)