Starting phenix.real_space_refine on Fri Aug 2 20:27:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlz_23914/08_2024/7mlz_23914.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlz_23914/08_2024/7mlz_23914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlz_23914/08_2024/7mlz_23914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlz_23914/08_2024/7mlz_23914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlz_23914/08_2024/7mlz_23914.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlz_23914/08_2024/7mlz_23914.cif" } resolution = 3.71 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= 0.006 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 22 5.16 5 C 3073 2.51 5 N 809 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4864 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.66, per 1000 atoms: 1.37 Number of scatterers: 4864 At special positions: 0 Unit cell: (86.427, 61.983, 138.807, 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 22 16.00 O 960 8.00 N 809 7.00 C 3073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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=2.05 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 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " 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: 1.98 Conformation dependent library (CDL) restraints added in 890.2 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 5.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.706A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.674A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.968A pdb=" N THR H 77 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.598A pdb=" N LEU L 125 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.689A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.599A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.896A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 38 removed outlier: 6.146A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 52 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.262A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER H 177 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA H 168 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER H 179 " --> pdb=" O PHE H 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 198 through 200 removed outlier: 3.504A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.825A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 37 removed outlier: 4.059A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.538A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 147 removed outlier: 3.520A pdb=" N GLU L 195 " --> pdb=" O GLN L 147 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1544 1.35 - 1.48: 1377 1.48 - 1.60: 2037 1.60 - 1.73: 0 1.73 - 1.85: 26 Bond restraints: 4984 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.73e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.34e+00 ... (remaining 4979 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.21: 199 107.21 - 113.91: 2719 113.91 - 120.60: 1785 120.60 - 127.30: 2022 127.30 - 133.99: 57 Bond angle restraints: 6782 Sorted by residual: angle pdb=" C THR H 191 " pdb=" N GLN H 192 " pdb=" CA GLN H 192 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.25e+01 angle pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C SER L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 angle pdb=" CA GLY H 55 " pdb=" C GLY H 55 " pdb=" N ASN H 56 " ideal model delta sigma weight residual 117.06 114.03 3.03 1.08e+00 8.57e-01 7.89e+00 ... (remaining 6777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 2835 22.98 - 45.97: 165 45.97 - 68.95: 14 68.95 - 91.94: 12 91.94 - 114.92: 4 Dihedral angle restraints: 3030 sinusoidal: 1225 harmonic: 1805 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 179.47 -86.47 1 1.00e+01 1.00e-02 9.01e+01 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 15.07 77.93 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 32.88 60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 3027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 568 0.051 - 0.101: 154 0.101 - 0.152: 35 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE L 48 " pdb=" CA ILE L 48 " pdb=" CG1 ILE L 48 " pdb=" CG2 ILE L 48 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS H 201 " pdb=" N LYS H 201 " pdb=" C LYS H 201 " pdb=" CB LYS H 201 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 760 not shown) Planarity restraints: 868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 112 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO L 113 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 429 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 429 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 429 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 429 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 429 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 429 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 429 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 412 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.027 5.00e-02 4.00e+02 ... (remaining 865 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 212 2.70 - 3.25: 5009 3.25 - 3.80: 7178 3.80 - 4.35: 9034 4.35 - 4.90: 14971 Nonbonded interactions: 36404 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" O CYS H 97 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR L 20 " pdb=" O LEU L 73 " model vdw 2.196 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.201 3.040 nonbonded pdb=" O ARG L 61 " pdb=" OG SER L 76 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OH TYR A 396 " model vdw 2.236 3.120 ... (remaining 36399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 22.930 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 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 : 0.004 0.055 4984 Z= 0.265 Angle : 0.821 8.116 6782 Z= 0.421 Chirality : 0.050 0.254 763 Planarity : 0.005 0.052 867 Dihedral : 14.730 114.921 1851 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.37 % Favored : 82.47 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.08 (0.31), residues: 616 helix: -4.58 (0.49), residues: 20 sheet: -2.30 (0.39), residues: 167 loop : -2.99 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS H 200 PHE 0.036 0.002 PHE A 429 TYR 0.029 0.002 TYR L 49 ARG 0.009 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8718 (mp) cc_final: 0.8491 (mm) REVERT: H 72 ASP cc_start: 0.7392 (t0) cc_final: 0.6045 (t0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2364 time to fit residues: 25.9403 Evaluate side-chains 69 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4984 Z= 0.247 Angle : 0.776 8.582 6782 Z= 0.396 Chirality : 0.049 0.180 763 Planarity : 0.006 0.050 867 Dihedral : 11.324 91.494 777 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.23 % Favored : 83.60 % Rotamer: Outliers : 1.31 % Allowed : 12.15 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.25 (0.30), residues: 616 helix: -4.10 (0.49), residues: 26 sheet: -2.32 (0.39), residues: 168 loop : -3.16 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 35 HIS 0.005 0.001 HIS L 189 PHE 0.024 0.002 PHE H 27 TYR 0.014 0.002 TYR H 96 ARG 0.008 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8766 (mp) cc_final: 0.8514 (mm) REVERT: H 72 ASP cc_start: 0.7889 (t0) cc_final: 0.7546 (t0) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.1993 time to fit residues: 20.3035 Evaluate side-chains 75 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.0020 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4984 Z= 0.224 Angle : 0.762 8.734 6782 Z= 0.385 Chirality : 0.048 0.162 763 Planarity : 0.005 0.049 867 Dihedral : 10.405 80.349 777 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.07 % Favored : 83.77 % Rotamer: Outliers : 0.93 % Allowed : 17.94 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.30 (0.30), residues: 616 helix: -3.97 (0.54), residues: 26 sheet: -2.27 (0.39), residues: 165 loop : -3.25 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.003 0.001 HIS L 189 PHE 0.027 0.002 PHE H 27 TYR 0.012 0.001 TYR A 453 ARG 0.007 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8784 (mp) cc_final: 0.8514 (mm) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 0.2010 time to fit residues: 20.7019 Evaluate side-chains 75 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.0370 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4984 Z= 0.247 Angle : 0.744 8.400 6782 Z= 0.381 Chirality : 0.048 0.162 763 Planarity : 0.005 0.048 867 Dihedral : 9.246 65.929 777 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.67 % Favored : 81.17 % Rotamer: Outliers : 2.06 % Allowed : 18.88 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.37 (0.29), residues: 616 helix: -3.84 (0.59), residues: 27 sheet: -2.32 (0.39), residues: 167 loop : -3.31 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.029 0.002 PHE H 27 TYR 0.018 0.002 TYR L 140 ARG 0.008 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8839 (mp) cc_final: 0.8572 (mm) REVERT: H 117 LYS cc_start: 0.7261 (pptt) cc_final: 0.6383 (pptt) REVERT: H 144 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7201 (t0) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.1860 time to fit residues: 21.2632 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4984 Z= 0.210 Angle : 0.743 8.140 6782 Z= 0.379 Chirality : 0.049 0.250 763 Planarity : 0.005 0.050 867 Dihedral : 8.157 58.799 777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.75 % Favored : 84.09 % Rotamer: Outliers : 3.18 % Allowed : 20.00 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.33 (0.30), residues: 616 helix: -3.71 (0.61), residues: 27 sheet: -2.39 (0.39), residues: 163 loop : -3.24 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.031 0.002 PHE H 27 TYR 0.018 0.001 TYR L 140 ARG 0.007 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8843 (mp) cc_final: 0.8582 (mm) REVERT: H 117 LYS cc_start: 0.7141 (pptt) cc_final: 0.6101 (pptt) REVERT: H 144 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7214 (t0) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 0.2203 time to fit residues: 25.7598 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 overall best weight: 0.3308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4984 Z= 0.187 Angle : 0.742 7.153 6782 Z= 0.378 Chirality : 0.048 0.164 763 Planarity : 0.005 0.048 867 Dihedral : 7.388 59.826 777 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.58 % Favored : 84.25 % Rotamer: Outliers : 2.99 % Allowed : 20.19 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.25 (0.30), residues: 616 helix: -3.74 (0.60), residues: 27 sheet: -2.39 (0.39), residues: 166 loop : -3.16 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 PHE 0.034 0.002 PHE H 27 TYR 0.018 0.001 TYR L 140 ARG 0.005 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8842 (mp) cc_final: 0.8568 (mm) REVERT: H 117 LYS cc_start: 0.6979 (pptt) cc_final: 0.6050 (pptt) REVERT: H 144 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7286 (t0) outliers start: 16 outliers final: 8 residues processed: 91 average time/residue: 0.1897 time to fit residues: 21.8737 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4984 Z= 0.206 Angle : 0.738 7.509 6782 Z= 0.376 Chirality : 0.047 0.158 763 Planarity : 0.005 0.049 867 Dihedral : 6.866 58.712 777 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.23 % Favored : 83.60 % Rotamer: Outliers : 2.43 % Allowed : 21.12 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.28 (0.30), residues: 616 helix: -3.68 (0.60), residues: 27 sheet: -2.36 (0.38), residues: 172 loop : -3.21 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS L 189 PHE 0.035 0.002 PHE H 27 TYR 0.020 0.001 TYR L 140 ARG 0.008 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8822 (mp) cc_final: 0.8553 (mm) REVERT: H 117 LYS cc_start: 0.7006 (pptt) cc_final: 0.6050 (pptt) REVERT: H 144 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7267 (t0) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.1983 time to fit residues: 21.4863 Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4984 Z= 0.225 Angle : 0.776 9.895 6782 Z= 0.390 Chirality : 0.049 0.369 763 Planarity : 0.005 0.049 867 Dihedral : 6.696 57.599 777 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.07 % Favored : 83.77 % Rotamer: Outliers : 2.43 % Allowed : 21.68 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.24 (0.30), residues: 616 helix: -3.44 (0.69), residues: 26 sheet: -2.35 (0.38), residues: 169 loop : -3.18 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.036 0.002 PHE H 27 TYR 0.019 0.001 TYR L 140 ARG 0.008 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8820 (mp) cc_final: 0.8554 (mm) REVERT: H 144 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: L 175 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7263 (mt) outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.1830 time to fit residues: 20.0411 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.0070 chunk 60 optimal weight: 0.0980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4984 Z= 0.203 Angle : 0.771 8.867 6782 Z= 0.388 Chirality : 0.049 0.297 763 Planarity : 0.005 0.049 867 Dihedral : 6.545 59.403 777 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.10 % Favored : 84.74 % Rotamer: Outliers : 2.43 % Allowed : 22.62 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.19 (0.30), residues: 616 helix: -3.54 (0.65), residues: 27 sheet: -2.37 (0.38), residues: 173 loop : -3.11 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS L 189 PHE 0.035 0.002 PHE H 27 TYR 0.017 0.001 TYR L 140 ARG 0.007 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8806 (mp) cc_final: 0.8545 (mm) REVERT: H 105 GLN cc_start: 0.7433 (pm20) cc_final: 0.7079 (pm20) REVERT: H 144 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: L 175 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7091 (mt) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 0.1754 time to fit residues: 18.7310 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6075 > 50: distance: 53 - 60: 4.076 distance: 60 - 61: 8.570 distance: 61 - 62: 6.562 distance: 61 - 64: 10.892 distance: 62 - 63: 18.401 distance: 62 - 69: 12.658 distance: 64 - 65: 4.964 distance: 65 - 66: 6.116 distance: 66 - 67: 7.744 distance: 67 - 68: 17.036 distance: 69 - 70: 6.329 distance: 69 - 75: 8.228 distance: 70 - 73: 4.176 distance: 71 - 72: 20.130 distance: 71 - 76: 26.831 distance: 73 - 74: 5.174 distance: 74 - 75: 6.170 distance: 76 - 77: 14.768 distance: 77 - 78: 5.471 distance: 78 - 79: 26.145 distance: 78 - 80: 17.246 distance: 80 - 81: 21.037 distance: 81 - 82: 8.668 distance: 81 - 84: 14.654 distance: 82 - 83: 23.239 distance: 82 - 89: 38.116 distance: 84 - 85: 24.293 distance: 86 - 87: 19.226 distance: 86 - 88: 4.872 distance: 89 - 90: 11.554 distance: 90 - 91: 22.169 distance: 91 - 92: 29.764 distance: 91 - 94: 13.529 distance: 94 - 100: 6.189 distance: 95 - 96: 17.832 distance: 95 - 98: 7.548 distance: 96 - 97: 10.477 distance: 96 - 101: 6.018 distance: 98 - 99: 10.904 distance: 99 - 100: 7.539 distance: 101 - 102: 7.051 distance: 102 - 103: 15.447 distance: 102 - 105: 7.476 distance: 103 - 104: 15.398 distance: 103 - 112: 10.279 distance: 105 - 106: 13.257 distance: 106 - 107: 11.360 distance: 107 - 108: 5.540 distance: 108 - 109: 8.947 distance: 109 - 110: 15.988 distance: 109 - 111: 6.545 distance: 112 - 113: 4.593 distance: 113 - 114: 8.045 distance: 113 - 116: 12.067 distance: 114 - 115: 15.643 distance: 114 - 120: 21.037 distance: 116 - 117: 8.178 distance: 117 - 118: 8.611 distance: 117 - 119: 12.910 distance: 120 - 121: 6.770 distance: 121 - 122: 8.018 distance: 121 - 124: 15.242 distance: 122 - 123: 25.347 distance: 122 - 128: 21.904 distance: 124 - 125: 14.516 distance: 125 - 126: 16.404 distance: 125 - 127: 33.084 distance: 128 - 129: 12.618 distance: 129 - 130: 4.480 distance: 129 - 132: 6.637 distance: 130 - 131: 15.526 distance: 130 - 136: 22.986 distance: 132 - 133: 7.315 distance: 132 - 134: 11.121