Starting phenix.real_space_refine on Fri Aug 2 18:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukn_20807/08_2024/6ukn_20807.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukn_20807/08_2024/6ukn_20807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukn_20807/08_2024/6ukn_20807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukn_20807/08_2024/6ukn_20807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukn_20807/08_2024/6ukn_20807.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukn_20807/08_2024/6ukn_20807.cif" } resolution = 3.65 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= 1.000 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 K 1 8.98 5 S 40 5.16 5 Cl 1 4.86 5 C 2689 2.51 5 N 639 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4109 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4029 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 514} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.95, per 1000 atoms: 0.72 Number of scatterers: 4109 At special positions: 0 Unit cell: (93.234, 68.22, 94.371, 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) K 1 19.00 Cl 1 17.00 S 40 16.00 O 739 8.00 N 639 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 352 " 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 C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 312 " " NAG C 1 " - " ASN A 360 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 732.6 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 66.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.599A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 4.286A pdb=" N PHE A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.852A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.629A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 Processing helix chain 'A' and resid 239 through 269 removed outlier: 4.421A pdb=" N ALA A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.579A pdb=" N VAL A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 421 through 428 removed outlier: 4.156A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.752A pdb=" N LEU A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Proline residue: A 452 - end of helix removed outlier: 3.942A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.783A pdb=" N ARG A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 504 through 536 removed outlier: 3.952A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.870A pdb=" N ASP A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 removed outlier: 4.038A pdb=" N GLN A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.842A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 560 " --> pdb=" O TRP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 removed outlier: 3.696A pdb=" N ALA A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 4.425A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 620 " --> pdb=" O TRP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 4.034A pdb=" N PHE A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 309 removed outlier: 4.046A pdb=" N ILE A 305 " --> pdb=" O GLY A 366 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 711 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: 1.08 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1233 1.35 - 1.47: 1103 1.47 - 1.59: 1805 1.59 - 1.71: 0 1.71 - 1.84: 60 Bond restraints: 4201 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" CG1 ILE A 221 " pdb=" CD1 ILE A 221 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.46e+00 bond pdb=" C PHE A 428 " pdb=" N PRO A 429 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.08e-02 8.57e+03 1.39e+00 ... (remaining 4196 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.77: 116 106.77 - 113.57: 2386 113.57 - 120.36: 1599 120.36 - 127.16: 1579 127.16 - 133.95: 43 Bond angle restraints: 5723 Sorted by residual: angle pdb=" C ASP A 484 " pdb=" N LYS A 485 " pdb=" CA LYS A 485 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" C LYS A 325 " pdb=" N MET A 326 " pdb=" CA MET A 326 " ideal model delta sigma weight residual 120.82 127.52 -6.70 1.50e+00 4.44e-01 2.00e+01 angle pdb=" C PHE A 420 " pdb=" N THR A 421 " pdb=" CA THR A 421 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" C VAL A 400 " pdb=" N SER A 401 " pdb=" CA SER A 401 " ideal model delta sigma weight residual 122.35 126.42 -4.07 1.46e+00 4.69e-01 7.79e+00 angle pdb=" C ALA A 350 " pdb=" N THR A 351 " pdb=" CA THR A 351 " ideal model delta sigma weight residual 122.46 126.36 -3.90 1.41e+00 5.03e-01 7.64e+00 ... (remaining 5718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 2316 22.88 - 45.75: 147 45.75 - 68.63: 10 68.63 - 91.51: 28 91.51 - 114.38: 16 Dihedral angle restraints: 2517 sinusoidal: 991 harmonic: 1526 Sorted by residual: dihedral pdb=" CA LYS A 325 " pdb=" C LYS A 325 " pdb=" N MET A 326 " pdb=" CA MET A 326 " ideal model delta harmonic sigma weight residual 180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLN A 327 " pdb=" C GLN A 327 " pdb=" N VAL A 328 " pdb=" CA VAL A 328 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 2514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 671 0.113 - 0.226: 26 0.226 - 0.339: 3 0.339 - 0.452: 0 0.452 - 0.564: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.27e+01 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.13e+01 ... (remaining 698 not shown) Planarity restraints: 696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 604 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 605 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 626 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C CYS A 626 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 626 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 627 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 428 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 429 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 ... (remaining 693 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1459 2.85 - 3.42: 4729 3.42 - 4.00: 7005 4.00 - 4.57: 10048 4.57 - 5.14: 14405 Nonbonded interactions: 37646 Sorted by model distance: nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.280 3.040 nonbonded pdb=" O SER A 511 " pdb=" OG1 THR A 515 " model vdw 2.302 3.040 nonbonded pdb=" O4 BMA B 3 " pdb=" O6 BMA B 3 " model vdw 2.347 3.040 nonbonded pdb=" OD2 ASP A 415 " pdb=" NZ LYS A 485 " model vdw 2.386 3.120 nonbonded pdb=" O SER A 231 " pdb=" OG SER A 231 " model vdw 2.407 3.040 ... (remaining 37641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 0.047 4201 Z= 0.346 Angle : 0.831 9.175 5723 Z= 0.447 Chirality : 0.055 0.564 701 Planarity : 0.006 0.066 694 Dihedral : 20.626 114.383 1538 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.47 % Allowed : 9.53 % Favored : 90.00 % 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: -2.59 (0.33), residues: 534 helix: -0.93 (0.25), residues: 333 sheet: -2.49 (1.44), residues: 10 loop : -3.02 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 505 HIS 0.004 0.002 HIS A 615 PHE 0.016 0.002 PHE A 428 TYR 0.011 0.001 TYR A 186 ARG 0.001 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 171 MET cc_start: 0.7574 (ttm) cc_final: 0.6959 (ttm) REVERT: A 279 VAL cc_start: 0.9342 (t) cc_final: 0.8915 (p) REVERT: A 435 MET cc_start: 0.8320 (mmt) cc_final: 0.7700 (mmt) REVERT: A 521 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 547 HIS cc_start: 0.7428 (m170) cc_final: 0.7073 (m170) REVERT: A 559 LEU cc_start: 0.8698 (tp) cc_final: 0.8481 (tp) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1384 time to fit residues: 21.8648 Evaluate side-chains 85 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4201 Z= 0.259 Angle : 0.740 7.980 5723 Z= 0.362 Chirality : 0.048 0.459 701 Planarity : 0.005 0.056 694 Dihedral : 18.211 100.829 693 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.26 % Allowed : 18.37 % Favored : 78.37 % 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 (0.36), residues: 534 helix: 0.38 (0.28), residues: 331 sheet: -1.94 (1.66), residues: 10 loop : -2.84 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 505 HIS 0.003 0.001 HIS A 615 PHE 0.014 0.001 PHE A 428 TYR 0.011 0.001 TYR A 186 ARG 0.002 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.431 Fit side-chains REVERT: A 186 TYR cc_start: 0.7901 (t80) cc_final: 0.7695 (t80) REVERT: A 262 MET cc_start: 0.8778 (mmm) cc_final: 0.8543 (mmm) REVERT: A 385 ASP cc_start: 0.8487 (t0) cc_final: 0.8283 (t0) REVERT: A 520 LEU cc_start: 0.9139 (mt) cc_final: 0.8931 (mt) REVERT: A 521 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 547 HIS cc_start: 0.7422 (m170) cc_final: 0.7089 (m170) REVERT: A 583 MET cc_start: 0.7501 (tmm) cc_final: 0.7187 (tmm) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.1014 time to fit residues: 15.5090 Evaluate side-chains 98 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4201 Z= 0.188 Angle : 0.686 7.680 5723 Z= 0.328 Chirality : 0.048 0.478 701 Planarity : 0.004 0.051 694 Dihedral : 15.375 94.803 693 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.12 % Allowed : 20.23 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.38), residues: 534 helix: 1.09 (0.29), residues: 325 sheet: -1.45 (1.71), residues: 10 loop : -2.77 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 PHE 0.013 0.001 PHE A 154 TYR 0.011 0.001 TYR A 614 ARG 0.001 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.436 Fit side-chains REVERT: A 171 MET cc_start: 0.7812 (ttp) cc_final: 0.6576 (ttm) REVERT: A 521 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 547 HIS cc_start: 0.7423 (m170) cc_final: 0.6964 (m90) outliers start: 22 outliers final: 11 residues processed: 113 average time/residue: 0.1140 time to fit residues: 17.3718 Evaluate side-chains 103 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4201 Z= 0.202 Angle : 0.689 7.620 5723 Z= 0.330 Chirality : 0.048 0.484 701 Planarity : 0.004 0.052 694 Dihedral : 14.056 90.996 693 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.26 % Allowed : 22.33 % Favored : 74.42 % 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: -0.19 (0.38), residues: 534 helix: 1.37 (0.30), residues: 325 sheet: -1.39 (1.73), residues: 10 loop : -2.75 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 635 HIS 0.002 0.001 HIS A 615 PHE 0.011 0.001 PHE A 428 TYR 0.009 0.001 TYR A 186 ARG 0.001 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.339 Fit side-chains REVERT: A 385 ASP cc_start: 0.8360 (t0) cc_final: 0.8032 (t0) REVERT: A 435 MET cc_start: 0.8230 (mmt) cc_final: 0.7972 (mmt) REVERT: A 521 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8489 (tm-30) REVERT: A 547 HIS cc_start: 0.7431 (m170) cc_final: 0.6970 (m90) outliers start: 14 outliers final: 11 residues processed: 108 average time/residue: 0.0897 time to fit residues: 13.2399 Evaluate side-chains 101 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4201 Z= 0.166 Angle : 0.643 7.243 5723 Z= 0.309 Chirality : 0.047 0.494 701 Planarity : 0.004 0.051 694 Dihedral : 12.786 86.113 693 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.19 % Allowed : 22.33 % Favored : 73.49 % 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: 0.12 (0.38), residues: 534 helix: 1.61 (0.30), residues: 327 sheet: -1.09 (1.75), residues: 10 loop : -2.66 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 PHE 0.011 0.001 PHE A 154 TYR 0.010 0.001 TYR A 272 ARG 0.002 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 262 MET cc_start: 0.8778 (tpp) cc_final: 0.8406 (mmm) REVERT: A 377 ASP cc_start: 0.6545 (t0) cc_final: 0.6331 (t0) REVERT: A 521 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 547 HIS cc_start: 0.7448 (m170) cc_final: 0.6990 (m90) REVERT: A 615 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.7423 (t-90) outliers start: 18 outliers final: 10 residues processed: 118 average time/residue: 0.0992 time to fit residues: 16.2514 Evaluate side-chains 106 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.0170 chunk 42 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4201 Z= 0.171 Angle : 0.666 7.289 5723 Z= 0.314 Chirality : 0.047 0.506 701 Planarity : 0.004 0.050 694 Dihedral : 11.890 81.359 693 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.72 % Allowed : 25.81 % Favored : 70.47 % 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: 0.26 (0.38), residues: 534 helix: 1.71 (0.30), residues: 326 sheet: -0.84 (1.80), residues: 10 loop : -2.58 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 635 HIS 0.001 0.000 HIS A 615 PHE 0.011 0.001 PHE A 154 TYR 0.007 0.001 TYR A 186 ARG 0.001 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 262 MET cc_start: 0.8786 (tpp) cc_final: 0.8445 (mmm) REVERT: A 297 LYS cc_start: 0.8375 (mptt) cc_final: 0.7836 (tmtt) REVERT: A 385 ASP cc_start: 0.8310 (t0) cc_final: 0.8048 (t0) REVERT: A 520 LEU cc_start: 0.9115 (mt) cc_final: 0.8786 (mt) REVERT: A 521 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 547 HIS cc_start: 0.7542 (m170) cc_final: 0.7030 (m90) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1106 time to fit residues: 16.3230 Evaluate side-chains 112 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 636 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.3309 > 50: distance: 8 - 82: 14.852 distance: 13 - 19: 28.892 distance: 19 - 20: 41.567 distance: 20 - 21: 48.641 distance: 20 - 23: 34.265 distance: 21 - 22: 18.431 distance: 21 - 24: 60.331 distance: 24 - 25: 30.778 distance: 25 - 26: 45.868 distance: 25 - 28: 16.889 distance: 26 - 27: 17.807 distance: 26 - 32: 19.271 distance: 28 - 29: 23.967 distance: 29 - 30: 12.893 distance: 29 - 31: 10.379 distance: 32 - 33: 16.227 distance: 33 - 34: 28.284 distance: 33 - 36: 33.012 distance: 34 - 35: 38.954 distance: 34 - 43: 10.052 distance: 36 - 37: 25.917 distance: 37 - 38: 26.824 distance: 38 - 39: 11.913 distance: 39 - 40: 15.864 distance: 40 - 41: 8.755 distance: 40 - 42: 7.788 distance: 43 - 44: 38.250 distance: 44 - 45: 50.593 distance: 44 - 47: 28.819 distance: 45 - 46: 36.659 distance: 45 - 51: 56.472 distance: 47 - 48: 25.778 distance: 48 - 49: 22.186 distance: 48 - 50: 13.868 distance: 51 - 52: 37.844 distance: 52 - 53: 38.468 distance: 52 - 55: 26.450 distance: 53 - 54: 31.924 distance: 53 - 62: 52.500 distance: 55 - 56: 16.609 distance: 56 - 57: 13.295 distance: 56 - 58: 7.933 distance: 57 - 59: 19.530 distance: 58 - 60: 7.659 distance: 59 - 61: 6.978 distance: 60 - 61: 13.145 distance: 62 - 63: 25.129 distance: 63 - 64: 38.764 distance: 63 - 66: 16.518 distance: 64 - 65: 24.800 distance: 64 - 70: 35.596 distance: 66 - 67: 10.821 distance: 67 - 68: 19.227 distance: 67 - 69: 20.812 distance: 70 - 71: 34.056 distance: 71 - 72: 41.202 distance: 71 - 74: 26.521 distance: 72 - 73: 57.949 distance: 72 - 77: 42.153 distance: 74 - 75: 31.857 distance: 74 - 76: 16.756 distance: 77 - 78: 50.948 distance: 78 - 79: 36.979 distance: 78 - 81: 18.977 distance: 79 - 80: 37.471 distance: 79 - 83: 43.754 distance: 81 - 82: 27.710 distance: 83 - 84: 42.332 distance: 84 - 85: 23.571 distance: 84 - 87: 18.774 distance: 85 - 86: 15.206 distance: 85 - 88: 3.120 distance: 88 - 89: 3.846 distance: 89 - 90: 19.913 distance: 89 - 92: 7.935 distance: 90 - 91: 9.454 distance: 90 - 97: 12.070 distance: 92 - 93: 18.772 distance: 93 - 94: 14.515 distance: 94 - 95: 19.604