Starting phenix.real_space_refine on Sun Mar 10 16:44:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/03_2024/7f62_31470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/03_2024/7f62_31470.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/7f62_31470/03_2024/7f62_31470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/03_2024/7f62_31470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/03_2024/7f62_31470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/03_2024/7f62_31470.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= -0.001 sd= 0.034 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 18 5.16 5 C 2104 2.51 5 N 552 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1579 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 2.27, per 1000 atoms: 0.68 Number of scatterers: 3321 At special positions: 0 Unit cell: (77, 53.9, 102.3, 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 18 16.00 O 647 8.00 N 552 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 616.6 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 9.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.007A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.936A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.197A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.625A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.075A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.998A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.919A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.072A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.133A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 35 through 36 removed outlier: 4.195A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.725A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 90 through 91 removed outlier: 3.741A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 68 hydrogen bonds defined for protein. 153 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: 0.78 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1046 1.34 - 1.46: 748 1.46 - 1.58: 1588 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 3406 Sorted by residual: bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.29e-02 6.01e+03 6.35e+00 bond pdb=" C ASN A 448 " pdb=" N TYR A 449 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 bond pdb=" C TYR A 449 " pdb=" O TYR A 449 " ideal model delta sigma weight residual 1.235 1.218 0.018 1.26e-02 6.30e+03 1.99e+00 bond pdb=" CE2 TYR A 449 " pdb=" CZ TYR A 449 " ideal model delta sigma weight residual 1.378 1.345 0.033 2.40e-02 1.74e+03 1.92e+00 bond pdb=" C SER L 95 " pdb=" O SER L 95 " ideal model delta sigma weight residual 1.241 1.231 0.011 9.80e-03 1.04e+04 1.19e+00 ... (remaining 3401 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.40: 93 106.40 - 113.29: 1753 113.29 - 120.18: 1159 120.18 - 127.07: 1584 127.07 - 133.96: 35 Bond angle restraints: 4624 Sorted by residual: angle pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 120.79 116.56 4.23 9.70e-01 1.06e+00 1.91e+01 angle pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta sigma weight residual 119.99 124.05 -4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" CA TYR A 449 " pdb=" CB TYR A 449 " pdb=" CG TYR A 449 " ideal model delta sigma weight residual 113.90 119.63 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" N LEU A 452 " pdb=" CA LEU A 452 " pdb=" C LEU A 452 " ideal model delta sigma weight residual 109.41 113.80 -4.39 1.52e+00 4.33e-01 8.32e+00 angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 120.65 124.21 -3.56 1.32e+00 5.74e-01 7.27e+00 ... (remaining 4619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1770 15.33 - 30.66: 174 30.66 - 45.99: 49 45.99 - 61.32: 12 61.32 - 76.65: 4 Dihedral angle restraints: 2009 sinusoidal: 771 harmonic: 1238 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 26.90 66.10 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CA GLN H 3 " pdb=" C GLN H 3 " pdb=" N LEU H 4 " pdb=" CA LEU H 4 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -132.09 46.09 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 308 0.032 - 0.063: 120 0.063 - 0.095: 41 0.095 - 0.127: 22 0.127 - 0.159: 4 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 492 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 448 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.02e+00 pdb=" C ASN A 448 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 448 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 449 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 521 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 14 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.020 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 44 2.52 - 3.11: 2497 3.11 - 3.71: 5200 3.71 - 4.30: 7066 4.30 - 4.90: 11389 Nonbonded interactions: 26196 Sorted by model distance: nonbonded pdb=" O VAL L 29 " pdb=" ND1 HIS L 93 " model vdw 1.925 2.520 nonbonded pdb=" CE2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.951 3.560 nonbonded pdb=" CD2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.983 3.560 nonbonded pdb=" OH TYR H 60 " pdb=" O THR H 65 " model vdw 2.177 2.440 nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.207 2.440 ... (remaining 26191 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: 2.320 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: 11.640 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3406 Z= 0.166 Angle : 0.649 6.271 4624 Z= 0.369 Chirality : 0.043 0.159 495 Planarity : 0.004 0.047 593 Dihedral : 13.209 76.650 1207 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 1.38 % Allowed : 1.65 % Favored : 96.97 % 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: -2.76 (0.39), residues: 419 helix: -4.04 (0.68), residues: 30 sheet: -0.91 (0.48), residues: 123 loop : -2.11 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 48 HIS 0.002 0.001 HIS L 35 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.001 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9212 (m-80) cc_final: 0.8985 (m-80) REVERT: A 451 TYR cc_start: 0.4870 (OUTLIER) cc_final: 0.4556 (m-10) REVERT: A 489 TYR cc_start: 0.7475 (m-80) cc_final: 0.7107 (m-10) REVERT: H 4 LEU cc_start: 0.6374 (mt) cc_final: 0.5859 (mp) REVERT: H 101 ASN cc_start: 0.7598 (p0) cc_final: 0.7169 (p0) REVERT: H 103 GLU cc_start: 0.7792 (tp30) cc_final: 0.7303 (tm-30) REVERT: L 75 THR cc_start: 0.7609 (t) cc_final: 0.7089 (m) outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.2469 time to fit residues: 27.4710 Evaluate side-chains 54 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain L residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN H 74 ASN L 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3406 Z= 0.204 Angle : 0.607 5.335 4624 Z= 0.315 Chirality : 0.045 0.142 495 Planarity : 0.004 0.046 593 Dihedral : 5.879 51.264 480 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.58 % Allowed : 12.12 % Favored : 84.30 % 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: -2.54 (0.39), residues: 419 helix: -3.73 (0.78), residues: 30 sheet: -0.95 (0.48), residues: 123 loop : -1.87 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 48 HIS 0.003 0.001 HIS L 35 PHE 0.016 0.002 PHE L 63 TYR 0.017 0.001 TYR H 95 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9208 (m-80) cc_final: 0.8964 (m-80) REVERT: A 424 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8090 (tptp) REVERT: A 480 CYS cc_start: 0.4183 (OUTLIER) cc_final: 0.3184 (m) REVERT: A 489 TYR cc_start: 0.7093 (m-80) cc_final: 0.6830 (m-10) REVERT: H 82 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: H 83 MET cc_start: 0.8451 (mtm) cc_final: 0.7765 (mtm) REVERT: H 103 GLU cc_start: 0.7524 (tp30) cc_final: 0.7247 (tm-30) REVERT: L 75 THR cc_start: 0.7138 (t) cc_final: 0.6922 (m) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.1576 time to fit residues: 12.0767 Evaluate side-chains 57 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 54 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3406 Z= 0.140 Angle : 0.556 6.098 4624 Z= 0.286 Chirality : 0.043 0.129 495 Planarity : 0.004 0.045 593 Dihedral : 4.408 20.847 472 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.86 % Allowed : 14.60 % Favored : 81.54 % 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: -2.20 (0.39), residues: 419 helix: -3.91 (0.67), residues: 30 sheet: -0.28 (0.53), residues: 109 loop : -1.76 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 48 HIS 0.002 0.001 HIS L 90 PHE 0.014 0.001 PHE L 63 TYR 0.009 0.001 TYR L 87 ARG 0.005 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9194 (m-80) cc_final: 0.8963 (m-80) REVERT: A 424 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8193 (tptp) REVERT: A 480 CYS cc_start: 0.3719 (OUTLIER) cc_final: 0.3364 (m) REVERT: H 82 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: H 83 MET cc_start: 0.8555 (mtm) cc_final: 0.8076 (mtm) REVERT: H 103 GLU cc_start: 0.7492 (tp30) cc_final: 0.7157 (tm-30) REVERT: L 62 ARG cc_start: 0.7029 (ttm110) cc_final: 0.6232 (ptm-80) REVERT: L 75 THR cc_start: 0.7278 (t) cc_final: 0.6980 (m) REVERT: L 83 ASP cc_start: 0.4644 (t70) cc_final: 0.4441 (t70) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.2029 time to fit residues: 16.3643 Evaluate side-chains 62 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 49 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3406 Z= 0.269 Angle : 0.646 9.188 4624 Z= 0.332 Chirality : 0.045 0.147 495 Planarity : 0.005 0.045 593 Dihedral : 4.954 19.577 472 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 6.61 % Allowed : 17.63 % Favored : 75.76 % 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: -2.18 (0.39), residues: 419 helix: -3.95 (0.68), residues: 24 sheet: -0.38 (0.51), residues: 105 loop : -1.74 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 48 HIS 0.005 0.002 HIS L 90 PHE 0.014 0.002 PHE H 29 TYR 0.012 0.002 TYR H 95 ARG 0.005 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.8460 (tmtt) cc_final: 0.8145 (tptp) REVERT: H 82 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: H 83 MET cc_start: 0.8322 (mtm) cc_final: 0.7998 (mtm) REVERT: L 75 THR cc_start: 0.7393 (t) cc_final: 0.7059 (m) REVERT: L 94 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8615 (mtp180) outliers start: 24 outliers final: 14 residues processed: 63 average time/residue: 0.1551 time to fit residues: 12.0793 Evaluate side-chains 58 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3406 Z= 0.136 Angle : 0.544 6.675 4624 Z= 0.278 Chirality : 0.043 0.143 495 Planarity : 0.004 0.045 593 Dihedral : 4.491 16.658 472 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.41 % Allowed : 19.56 % Favored : 76.03 % 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: -2.01 (0.39), residues: 419 helix: -3.80 (0.69), residues: 24 sheet: 0.12 (0.54), residues: 101 loop : -1.77 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 48 HIS 0.002 0.001 HIS L 93 PHE 0.013 0.001 PHE H 68 TYR 0.018 0.001 TYR H 95 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: A 529 LYS cc_start: 0.9282 (mmmm) cc_final: 0.9059 (mmmm) REVERT: H 11 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6601 (pp) REVERT: H 60 TYR cc_start: 0.7639 (p90) cc_final: 0.7078 (p90) REVERT: H 82 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: H 83 MET cc_start: 0.8411 (mtm) cc_final: 0.8146 (mtm) REVERT: L 75 THR cc_start: 0.7203 (t) cc_final: 0.6821 (m) REVERT: L 91 GLN cc_start: 0.7981 (pp30) cc_final: 0.7567 (pp30) REVERT: L 94 ARG cc_start: 0.8833 (mtp-110) cc_final: 0.8456 (mmm-85) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.1804 time to fit residues: 12.8289 Evaluate side-chains 55 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3406 Z= 0.356 Angle : 0.655 7.784 4624 Z= 0.350 Chirality : 0.046 0.154 495 Planarity : 0.005 0.045 593 Dihedral : 5.353 17.715 472 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 5.79 % Allowed : 20.39 % Favored : 73.83 % 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: -2.38 (0.38), residues: 419 helix: -3.41 (0.83), residues: 24 sheet: -0.53 (0.53), residues: 103 loop : -1.94 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 36 HIS 0.004 0.002 HIS L 90 PHE 0.011 0.002 PHE H 29 TYR 0.014 0.002 TYR H 95 ARG 0.009 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 424 LYS cc_start: 0.8510 (tmtt) cc_final: 0.8087 (tptp) REVERT: H 60 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6821 (p90) outliers start: 21 outliers final: 15 residues processed: 59 average time/residue: 0.1821 time to fit residues: 12.9448 Evaluate side-chains 54 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3406 Z= 0.247 Angle : 0.618 7.711 4624 Z= 0.320 Chirality : 0.045 0.150 495 Planarity : 0.005 0.043 593 Dihedral : 5.083 17.835 472 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.41 % Allowed : 22.31 % Favored : 73.28 % 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: -2.42 (0.38), residues: 419 helix: -3.32 (0.84), residues: 24 sheet: -0.72 (0.52), residues: 110 loop : -1.93 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 36 HIS 0.002 0.001 HIS L 90 PHE 0.012 0.001 PHE L 63 TYR 0.016 0.001 TYR H 95 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.8510 (tmtt) cc_final: 0.8137 (tptp) REVERT: H 60 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6790 (p90) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.1820 time to fit residues: 11.6328 Evaluate side-chains 56 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 52.0281 > 50: distance: 13 - 168: 10.826 distance: 35 - 172: 4.227 distance: 38 - 169: 3.106 distance: 55 - 154: 6.943 distance: 58 - 151: 9.294 distance: 73 - 134: 7.213 distance: 76 - 131: 8.399 distance: 111 - 112: 4.008 distance: 113 - 114: 5.783 distance: 113 - 119: 5.600 distance: 115 - 116: 6.341 distance: 116 - 117: 4.632 distance: 116 - 118: 4.142 distance: 119 - 120: 7.168 distance: 120 - 121: 8.596 distance: 120 - 123: 4.948 distance: 121 - 122: 31.974 distance: 121 - 126: 22.487 distance: 123 - 124: 4.177 distance: 123 - 125: 15.474 distance: 126 - 127: 18.093 distance: 126 - 252: 29.134 distance: 127 - 128: 29.837 distance: 127 - 130: 40.688 distance: 128 - 129: 6.286 distance: 128 - 131: 8.182 distance: 129 - 249: 13.765 distance: 131 - 132: 4.769 distance: 132 - 133: 4.856 distance: 132 - 135: 3.901 distance: 133 - 134: 7.005 distance: 133 - 139: 4.989 distance: 135 - 136: 3.179 distance: 136 - 137: 5.856 distance: 137 - 138: 7.099 distance: 139 - 140: 3.349 distance: 139 - 241: 3.173 distance: 140 - 143: 5.279 distance: 141 - 142: 16.441 distance: 141 - 151: 4.038 distance: 142 - 238: 16.362 distance: 143 - 144: 3.896 distance: 144 - 145: 3.098 distance: 144 - 146: 8.810 distance: 145 - 147: 5.075 distance: 146 - 148: 11.953 distance: 147 - 149: 3.509 distance: 151 - 152: 4.980 distance: 152 - 153: 7.774 distance: 152 - 155: 3.197 distance: 153 - 154: 6.541 distance: 153 - 163: 5.748 distance: 155 - 156: 5.830 distance: 156 - 157: 5.312 distance: 156 - 158: 3.494 distance: 157 - 159: 4.115 distance: 159 - 161: 5.196 distance: 160 - 161: 3.956 distance: 161 - 162: 3.547 distance: 163 - 164: 6.246 distance: 164 - 165: 5.177 distance: 164 - 167: 5.231 distance: 165 - 166: 6.786 distance: 167 - 168: 8.507 distance: 169 - 170: 3.023 distance: 170 - 171: 3.240 distance: 170 - 173: 8.705 distance: 171 - 172: 3.808 distance: 171 - 174: 3.477 distance: 175 - 178: 7.215 distance: 176 - 177: 8.951 distance: 176 - 182: 4.015 distance: 178 - 179: 6.033 distance: 179 - 180: 7.603 distance: 179 - 181: 8.308 distance: 182 - 183: 3.888 distance: 183 - 184: 3.534 distance: 183 - 186: 4.484 distance: 184 - 185: 7.257 distance: 184 - 193: 4.270 distance: 186 - 187: 3.476 distance: 187 - 188: 9.318 distance: 189 - 191: 8.611 distance: 190 - 192: 7.407 distance: 191 - 192: 8.475