Starting phenix.real_space_refine on Wed Jan 17 12:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/01_2024/7jva_22497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/01_2024/7jva_22497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/01_2024/7jva_22497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/01_2024/7jva_22497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/01_2024/7jva_22497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/01_2024/7jva_22497.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 15 5.16 5 C 2068 2.51 5 N 548 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 1": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 62": "NH1" <-> "NH2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3248 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1495 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 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 Time building chain proxies: 2.28, per 1000 atoms: 0.70 Number of scatterers: 3248 At special positions: 0 Unit cell: (89.25, 75.6, 70.35, 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 15 16.00 O 617 8.00 N 548 7.00 C 2068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.09 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.07 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-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 623.6 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 13.3% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 28 through 32 removed outlier: 4.028A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.358A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.815A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.922A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.951A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.530A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 129 hydrogen bonds defined for protein. 285 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: 0.88 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 586 1.31 - 1.45: 1042 1.45 - 1.58: 1682 1.58 - 1.71: 4 1.71 - 1.84: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" CD GLU H 6 " pdb=" OE2 GLU H 6 " ideal model delta sigma weight residual 1.249 1.182 0.067 1.90e-02 2.77e+03 1.23e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 9.92e+00 bond pdb=" CB ASN H 50 " pdb=" CG ASN H 50 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 9.89e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 9.85e+00 bond pdb=" NE ARG A 357 " pdb=" CZ ARG A 357 " ideal model delta sigma weight residual 1.326 1.360 -0.034 1.10e-02 8.26e+03 9.59e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.77: 111 106.77 - 113.54: 1671 113.54 - 120.32: 1366 120.32 - 127.10: 1358 127.10 - 133.88: 33 Bond angle restraints: 4539 Sorted by residual: angle pdb=" CD1 LEU H 86 " pdb=" CG LEU H 86 " pdb=" CD2 LEU H 86 " ideal model delta sigma weight residual 110.80 131.55 -20.75 2.20e+00 2.07e-01 8.89e+01 angle pdb=" CG1 VAL H 2 " pdb=" CB VAL H 2 " pdb=" CG2 VAL H 2 " ideal model delta sigma weight residual 110.80 131.11 -20.31 2.20e+00 2.07e-01 8.52e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.02e+00 9.61e-01 5.60e+01 angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.85 126.34 -6.49 1.01e+00 9.80e-01 4.12e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.05 -6.49 1.02e+00 9.61e-01 4.04e+01 ... (remaining 4534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 1898 21.24 - 42.49: 57 42.49 - 63.73: 8 63.73 - 84.98: 8 84.98 - 106.22: 5 Dihedral angle restraints: 1976 sinusoidal: 767 harmonic: 1209 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -36.13 -49.87 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.51 106.22 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.96 105.58 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 1973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 422 0.112 - 0.224: 60 0.224 - 0.336: 9 0.336 - 0.448: 3 0.448 - 0.560: 2 Chirality restraints: 496 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 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 -2.48 0.08 2.00e-02 2.50e+03 1.68e+01 chirality pdb=" CG LEU H 86 " pdb=" CB LEU H 86 " pdb=" CD1 LEU H 86 " pdb=" CD2 LEU H 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 493 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 108 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR H 108 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 108 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR H 108 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 108 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 108 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 108 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 108 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.035 2.00e-02 2.50e+03 1.83e-02 6.70e+00 pdb=" CG TYR A 495 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 37 " 0.027 2.00e-02 2.50e+03 1.51e-02 4.59e+00 pdb=" CG TYR L 37 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR L 37 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR L 37 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR L 37 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 37 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR L 37 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 37 " 0.024 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1320 2.90 - 3.40: 2801 3.40 - 3.90: 5451 3.90 - 4.40: 6366 4.40 - 4.90: 10508 Nonbonded interactions: 26446 Sorted by model distance: nonbonded pdb=" OD2 ASP L 52 " pdb=" NZ LYS A 378 " model vdw 2.398 2.520 nonbonded pdb=" OE2 GLU H 6 " pdb=" N GLN H 111 " model vdw 2.536 2.520 nonbonded pdb=" N ASN A 440 " pdb=" OD1 ASN A 440 " model vdw 2.551 2.520 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.552 2.520 nonbonded pdb=" N CYS H 96 " pdb=" O CYS H 96 " model vdw 2.557 2.496 ... (remaining 26441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.000 Extract box with map and model: 11.050 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.016 0.079 3332 Z= 1.020 Angle : 1.515 20.747 4539 Z= 0.982 Chirality : 0.093 0.560 496 Planarity : 0.006 0.034 585 Dihedral : 13.100 106.220 1192 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.97 % Favored : 98.79 % Rotamer: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.43), residues: 412 helix: -4.22 (0.39), residues: 28 sheet: 0.47 (0.42), residues: 154 loop : 1.57 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP H 33 HIS 0.002 0.001 HIS L 8 PHE 0.024 0.004 PHE H 29 TYR 0.036 0.006 TYR H 108 ARG 0.007 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 91 THR cc_start: 0.8640 (m) cc_final: 0.8342 (t) REVERT: L 37 TYR cc_start: 0.9058 (m-80) cc_final: 0.8676 (m-10) REVERT: A 375 SER cc_start: 0.8854 (m) cc_final: 0.8575 (t) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1987 time to fit residues: 23.1281 Evaluate side-chains 64 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3332 Z= 0.325 Angle : 0.699 9.133 4539 Z= 0.368 Chirality : 0.048 0.144 496 Planarity : 0.004 0.032 585 Dihedral : 8.877 58.288 525 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.97 % Favored : 98.79 % Rotamer: Outliers : 3.05 % Allowed : 10.37 % Favored : 86.59 % 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 (0.42), residues: 412 helix: -3.51 (0.65), residues: 28 sheet: 0.23 (0.40), residues: 152 loop : 1.10 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 33 HIS 0.003 0.001 HIS L 99 PHE 0.012 0.002 PHE L 63 TYR 0.021 0.002 TYR H 32 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9061 (m-80) cc_final: 0.8855 (m-80) REVERT: H 91 THR cc_start: 0.8666 (m) cc_final: 0.8437 (t) REVERT: L 37 TYR cc_start: 0.9008 (m-80) cc_final: 0.8762 (m-10) REVERT: A 375 SER cc_start: 0.8946 (m) cc_final: 0.8596 (t) REVERT: A 441 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8297 (mp) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.1514 time to fit residues: 15.5896 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 HIS A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3332 Z= 0.274 Angle : 0.668 11.200 4539 Z= 0.337 Chirality : 0.047 0.164 496 Planarity : 0.004 0.036 585 Dihedral : 6.979 36.608 523 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.49 % Allowed : 10.37 % Favored : 84.15 % 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 (0.41), residues: 412 helix: -3.36 (0.72), residues: 28 sheet: 0.16 (0.42), residues: 149 loop : 0.80 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 33 HIS 0.004 0.002 HIS L 99 PHE 0.016 0.002 PHE H 68 TYR 0.014 0.002 TYR A 495 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9054 (m-80) cc_final: 0.8843 (m-80) REVERT: A 375 SER cc_start: 0.8975 (m) cc_final: 0.8620 (t) REVERT: A 506 GLN cc_start: 0.8305 (mp10) cc_final: 0.7848 (mp10) outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 0.1420 time to fit residues: 14.6607 Evaluate side-chains 70 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 17 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3332 Z= 0.221 Angle : 0.634 11.328 4539 Z= 0.315 Chirality : 0.045 0.152 496 Planarity : 0.004 0.038 585 Dihedral : 5.860 33.799 523 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.27 % Allowed : 12.20 % Favored : 83.54 % 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: 0.08 (0.41), residues: 412 helix: -3.22 (0.75), residues: 28 sheet: 0.00 (0.42), residues: 149 loop : 0.72 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.003 0.001 HIS L 99 PHE 0.008 0.001 PHE A 456 TYR 0.012 0.001 TYR A 369 ARG 0.006 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 109 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 375 SER cc_start: 0.8960 (m) cc_final: 0.8653 (t) REVERT: A 506 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8021 (mp10) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.1379 time to fit residues: 12.8646 Evaluate side-chains 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3332 Z= 0.343 Angle : 0.677 11.344 4539 Z= 0.340 Chirality : 0.047 0.169 496 Planarity : 0.004 0.039 585 Dihedral : 5.779 35.292 523 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.27 % Allowed : 14.02 % Favored : 81.71 % 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: -0.10 (0.41), residues: 412 helix: -2.77 (0.98), residues: 21 sheet: -0.23 (0.43), residues: 149 loop : 0.47 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 101 HIS 0.005 0.002 HIS A 519 PHE 0.012 0.002 PHE A 456 TYR 0.015 0.002 TYR A 453 ARG 0.012 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6662 (mp0) cc_final: 0.6405 (mp0) REVERT: L 109 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 375 SER cc_start: 0.8967 (m) cc_final: 0.8727 (t) REVERT: A 506 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8224 (mp10) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.1407 time to fit residues: 13.0540 Evaluate side-chains 78 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3332 Z= 0.276 Angle : 0.644 11.638 4539 Z= 0.322 Chirality : 0.045 0.165 496 Planarity : 0.004 0.039 585 Dihedral : 5.656 36.820 523 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.66 % Allowed : 15.85 % Favored : 80.49 % 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: -0.21 (0.42), residues: 412 helix: -2.54 (1.08), residues: 21 sheet: -0.37 (0.44), residues: 149 loop : 0.42 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.003 0.002 HIS A 519 PHE 0.012 0.001 PHE A 456 TYR 0.017 0.002 TYR A 508 ARG 0.005 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 109 THR cc_start: 0.8811 (m) cc_final: 0.8580 (p) REVERT: A 375 SER cc_start: 0.9084 (m) cc_final: 0.8766 (t) REVERT: A 506 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8266 (mp10) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1374 time to fit residues: 13.1224 Evaluate side-chains 77 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 3332 Z= 0.368 Angle : 0.685 11.581 4539 Z= 0.347 Chirality : 0.046 0.178 496 Planarity : 0.004 0.039 585 Dihedral : 5.854 38.890 523 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.66 % Allowed : 17.07 % Favored : 79.27 % 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: -0.46 (0.42), residues: 412 helix: -2.56 (1.09), residues: 21 sheet: -0.54 (0.45), residues: 142 loop : 0.19 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.005 0.002 HIS A 519 PHE 0.016 0.002 PHE A 456 TYR 0.021 0.002 TYR A 508 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (mp10) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1410 time to fit residues: 13.7460 Evaluate side-chains 76 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 53.8756 > 50: distance: 66 - 71: 7.711 distance: 71 - 72: 10.590 distance: 72 - 73: 17.231 distance: 72 - 75: 21.728 distance: 73 - 74: 13.470 distance: 73 - 79: 10.097 distance: 75 - 76: 15.981 distance: 76 - 77: 5.963 distance: 76 - 78: 6.628 distance: 79 - 80: 11.224 distance: 79 - 223: 8.754 distance: 80 - 81: 11.666 distance: 80 - 83: 8.426 distance: 81 - 82: 15.770 distance: 81 - 91: 10.345 distance: 82 - 220: 13.095 distance: 83 - 84: 11.609 distance: 84 - 85: 17.003 distance: 84 - 86: 14.814 distance: 85 - 87: 12.576 distance: 86 - 88: 4.968 distance: 87 - 89: 4.664 distance: 88 - 89: 7.479 distance: 89 - 90: 11.217 distance: 91 - 92: 5.596 distance: 92 - 93: 10.216 distance: 92 - 95: 9.788 distance: 93 - 94: 10.502 distance: 93 - 102: 8.445 distance: 95 - 96: 13.155 distance: 96 - 97: 10.525 distance: 97 - 98: 16.680 distance: 98 - 99: 11.914 distance: 99 - 100: 8.971 distance: 99 - 101: 11.007 distance: 102 - 103: 29.124 distance: 103 - 104: 40.836 distance: 103 - 106: 53.876 distance: 104 - 105: 15.583 distance: 104 - 110: 12.944 distance: 106 - 107: 44.135 distance: 107 - 108: 22.493 distance: 107 - 109: 28.173 distance: 110 - 111: 20.586 distance: 111 - 112: 8.246 distance: 111 - 114: 15.073 distance: 112 - 113: 7.486 distance: 112 - 121: 14.238 distance: 114 - 115: 8.846 distance: 115 - 116: 6.655 distance: 115 - 117: 13.848 distance: 116 - 118: 4.596 distance: 117 - 119: 10.277 distance: 118 - 120: 5.841 distance: 119 - 120: 12.771 distance: 121 - 122: 12.224 distance: 122 - 123: 11.655 distance: 122 - 125: 8.638 distance: 123 - 124: 6.624 distance: 123 - 132: 4.280 distance: 125 - 126: 6.851 distance: 126 - 127: 8.053 distance: 127 - 128: 3.069 distance: 128 - 129: 6.458 distance: 129 - 130: 5.791 distance: 129 - 131: 8.888 distance: 132 - 133: 4.196 distance: 133 - 134: 3.653 distance: 133 - 136: 5.929 distance: 134 - 135: 11.502 distance: 134 - 141: 8.745 distance: 136 - 137: 8.743 distance: 137 - 138: 10.050 distance: 138 - 139: 14.058 distance: 139 - 140: 5.299 distance: 142 - 143: 7.308 distance: 142 - 145: 5.769 distance: 143 - 144: 11.487 distance: 146 - 147: 10.411 distance: 147 - 148: 12.470 distance: 147 - 150: 8.864 distance: 148 - 149: 5.927 distance: 148 - 154: 14.181 distance: 150 - 151: 8.097 distance: 151 - 152: 4.631 distance: 151 - 153: 9.384 distance: 154 - 155: 8.224 distance: 155 - 156: 16.534 distance: 156 - 157: 19.772 distance: 156 - 162: 8.759 distance: 159 - 160: 3.211 distance: 159 - 161: 5.932