Starting phenix.real_space_refine on Fri Dec 8 01:47:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/12_2023/6l48_0832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/12_2023/6l48_0832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/12_2023/6l48_0832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/12_2023/6l48_0832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/12_2023/6l48_0832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/12_2023/6l48_0832_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 36 5.16 5 C 4482 2.51 5 N 1000 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6528 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3236 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3236 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.03, per 1000 atoms: 0.62 Number of scatterers: 6528 At special positions: 0 Unit cell: (141.075, 74.195, 72.105, 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 36 16.00 O 1010 8.00 N 1000 7.00 C 4482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 181 through 212 Proline residue: A 199 - end of helix removed outlier: 4.113A pdb=" N THR A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.865A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Proline residue: A 239 - end of helix removed outlier: 3.702A pdb=" N VAL A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 283 removed outlier: 3.858A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.182A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 343 Processing helix chain 'A' and resid 359 through 394 removed outlier: 4.234A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.782A pdb=" N ARG A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 438 Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.672A pdb=" N PHE A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 525 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 181 through 212 Proline residue: B 199 - end of helix removed outlier: 4.113A pdb=" N THR B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 209 " --> pdb=" O HIS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.865A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Proline residue: B 239 - end of helix removed outlier: 3.701A pdb=" N VAL B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 283 removed outlier: 3.858A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.182A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 343 Processing helix chain 'B' and resid 359 through 394 removed outlier: 4.234A pdb=" N ILE B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.781A pdb=" N ARG B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 Processing helix chain 'B' and resid 445 through 468 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.672A pdb=" N PHE B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 525 418 hydrogen bonds defined for protein. 1254 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: 1.78 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1831 1.34 - 1.46: 2056 1.46 - 1.58: 2835 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6780 Sorted by residual: bond pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 1.523 1.551 -0.027 1.30e-02 5.92e+03 4.39e+00 bond pdb=" CA ARG A 309 " pdb=" C ARG A 309 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.30e-02 5.92e+03 4.38e+00 bond pdb=" C13 CLR B2001 " pdb=" C14 CLR B2001 " ideal model delta sigma weight residual 1.537 1.509 0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C13 CLR A2001 " pdb=" C14 CLR A2001 " ideal model delta sigma weight residual 1.537 1.510 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" N ASP A 310 " pdb=" CA ASP A 310 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.64e+00 ... (remaining 6775 not shown) Histogram of bond angle deviations from ideal: 100.87 - 107.50: 294 107.50 - 114.12: 3672 114.12 - 120.75: 3297 120.75 - 127.38: 1911 127.38 - 134.01: 98 Bond angle restraints: 9272 Sorted by residual: angle pdb=" N ARG B 309 " pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 111.28 104.58 6.70 1.09e+00 8.42e-01 3.78e+01 angle pdb=" N ARG A 309 " pdb=" CA ARG A 309 " pdb=" C ARG A 309 " ideal model delta sigma weight residual 111.28 104.59 6.69 1.09e+00 8.42e-01 3.76e+01 angle pdb=" C TRP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 122.38 113.90 8.48 1.81e+00 3.05e-01 2.19e+01 angle pdb=" C TRP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 122.38 113.92 8.46 1.81e+00 3.05e-01 2.19e+01 angle pdb=" N ASP A 310 " pdb=" CA ASP A 310 " pdb=" C ASP A 310 " ideal model delta sigma weight residual 110.80 119.11 -8.31 2.13e+00 2.20e-01 1.52e+01 ... (remaining 9267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.42: 3462 14.42 - 28.84: 297 28.84 - 43.26: 85 43.26 - 57.67: 10 57.67 - 72.09: 2 Dihedral angle restraints: 3856 sinusoidal: 1482 harmonic: 2374 Sorted by residual: dihedral pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CA ASP A 310 " pdb=" CB ASP A 310 " ideal model delta harmonic sigma weight residual 122.80 134.29 -11.49 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" N ASP B 310 " pdb=" C ASP B 310 " pdb=" CA ASP B 310 " pdb=" CB ASP B 310 " ideal model delta harmonic sigma weight residual 122.80 134.29 -11.49 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" CA GLN A 354 " pdb=" C GLN A 354 " pdb=" N GLU A 355 " pdb=" CA GLU A 355 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 988 0.100 - 0.201: 30 0.201 - 0.301: 2 0.301 - 0.401: 0 0.401 - 0.502: 2 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CA ASP A 310 " pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CB ASP A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA ASP B 310 " pdb=" N ASP B 310 " pdb=" C ASP B 310 " pdb=" CB ASP B 310 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CA ARG B 309 " pdb=" N ARG B 309 " pdb=" C ARG B 309 " pdb=" CB ARG B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1019 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 308 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C TYR B 308 " 0.069 2.00e-02 2.50e+03 pdb=" O TYR B 308 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG B 309 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 308 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C TYR A 308 " -0.068 2.00e-02 2.50e+03 pdb=" O TYR A 308 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 309 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 389 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C LEU A 389 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 389 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 390 " 0.017 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 852 2.75 - 3.29: 6827 3.29 - 3.83: 11259 3.83 - 4.36: 12462 4.36 - 4.90: 21552 Nonbonded interactions: 52952 Sorted by model distance: nonbonded pdb=" OD2 ASP B 130 " pdb=" OH TYR B 322 " model vdw 2.217 2.440 nonbonded pdb=" OD2 ASP A 130 " pdb=" OH TYR A 322 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR B 299 " pdb=" O LEU B 396 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 299 " pdb=" O LEU A 396 " model vdw 2.283 2.440 nonbonded pdb=" O PHE A 237 " pdb=" N TYR A 241 " model vdw 2.284 2.520 ... (remaining 52947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.080 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.760 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 0.035 6780 Z= 0.209 Angle : 0.762 9.490 9272 Z= 0.404 Chirality : 0.050 0.502 1022 Planarity : 0.006 0.040 1100 Dihedral : 12.004 72.093 2324 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.45 % Allowed : 7.34 % Favored : 90.21 % Cbeta Deviations : 0.26 % 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: -3.38 (0.26), residues: 782 helix: -1.58 (0.18), residues: 600 sheet: None (None), residues: 0 loop : -4.04 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 504 HIS 0.008 0.001 HIS A 425 PHE 0.015 0.001 PHE A 331 TYR 0.013 0.001 TYR B 433 ARG 0.003 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 0.786 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 233 average time/residue: 0.2203 time to fit residues: 67.4540 Evaluate side-chains 134 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0632 time to fit residues: 1.7265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS A 296 GLN A 511 ASN B 204 GLN B 268 HIS B 296 GLN B 511 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6780 Z= 0.198 Angle : 0.684 13.132 9272 Z= 0.335 Chirality : 0.041 0.188 1022 Planarity : 0.005 0.043 1100 Dihedral : 5.127 22.027 1004 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.59 % Allowed : 16.36 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.30), residues: 782 helix: -0.27 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -3.57 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.009 0.002 HIS A 205 PHE 0.028 0.002 PHE A 398 TYR 0.016 0.001 TYR B 336 ARG 0.002 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.803 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 151 average time/residue: 0.1742 time to fit residues: 36.1661 Evaluate side-chains 138 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0638 time to fit residues: 3.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6780 Z= 0.180 Angle : 0.665 12.710 9272 Z= 0.318 Chirality : 0.040 0.141 1022 Planarity : 0.005 0.043 1100 Dihedral : 4.782 20.553 1004 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.06 % Allowed : 17.58 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.31), residues: 782 helix: 0.17 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.70 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.005 0.001 HIS A 205 PHE 0.019 0.001 PHE B 398 TYR 0.013 0.001 TYR A 336 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.736 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 153 average time/residue: 0.1592 time to fit residues: 33.4236 Evaluate side-chains 137 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0619 time to fit residues: 2.4497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 0.0470 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6780 Z= 0.184 Angle : 0.664 12.856 9272 Z= 0.316 Chirality : 0.041 0.189 1022 Planarity : 0.005 0.061 1100 Dihedral : 4.690 18.802 1004 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.45 % Allowed : 19.72 % Favored : 77.83 % 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: -0.82 (0.31), residues: 782 helix: 0.36 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.44 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 188 HIS 0.005 0.001 HIS B 425 PHE 0.021 0.001 PHE B 254 TYR 0.012 0.001 TYR B 430 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.726 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 143 average time/residue: 0.1743 time to fit residues: 33.6246 Evaluate side-chains 134 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0619 time to fit residues: 2.1433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 14 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: A 205 HIS A 368 ASN B 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6780 Z= 0.204 Angle : 0.675 11.787 9272 Z= 0.324 Chirality : 0.041 0.142 1022 Planarity : 0.005 0.048 1100 Dihedral : 4.675 17.857 1004 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.53 % Allowed : 21.71 % Favored : 76.76 % 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: -0.66 (0.31), residues: 782 helix: 0.48 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -3.29 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 427 HIS 0.008 0.001 HIS B 205 PHE 0.019 0.001 PHE A 398 TYR 0.015 0.001 TYR B 336 ARG 0.007 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.698 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 136 average time/residue: 0.1550 time to fit residues: 29.4883 Evaluate side-chains 125 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0617 time to fit residues: 1.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6780 Z= 0.237 Angle : 0.682 10.933 9272 Z= 0.330 Chirality : 0.042 0.150 1022 Planarity : 0.005 0.047 1100 Dihedral : 4.719 17.818 1004 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.45 % Allowed : 21.87 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.31), residues: 782 helix: 0.39 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.07 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.008 0.001 HIS A 205 PHE 0.022 0.001 PHE B 481 TYR 0.023 0.001 TYR A 430 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.670 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 134 average time/residue: 0.1395 time to fit residues: 26.3305 Evaluate side-chains 120 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0620 time to fit residues: 1.5460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6780 Z= 0.222 Angle : 0.668 10.537 9272 Z= 0.325 Chirality : 0.042 0.207 1022 Planarity : 0.005 0.046 1100 Dihedral : 4.596 16.508 1004 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.14 % Allowed : 22.48 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.31), residues: 782 helix: 0.42 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.99 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 427 HIS 0.007 0.001 HIS A 205 PHE 0.030 0.001 PHE B 481 TYR 0.012 0.001 TYR B 308 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.701 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.1575 time to fit residues: 29.0164 Evaluate side-chains 125 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0616 time to fit residues: 1.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 215 HIS B 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6780 Z= 0.201 Angle : 0.655 10.253 9272 Z= 0.318 Chirality : 0.041 0.177 1022 Planarity : 0.005 0.045 1100 Dihedral : 4.464 17.065 1004 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.68 % Allowed : 22.48 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.31), residues: 782 helix: 0.46 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -2.96 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.008 0.001 HIS A 205 PHE 0.033 0.001 PHE A 481 TYR 0.013 0.001 TYR A 308 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.711 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 130 average time/residue: 0.1604 time to fit residues: 28.8851 Evaluate side-chains 125 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0674 time to fit residues: 1.5677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6780 Z= 0.201 Angle : 0.653 10.157 9272 Z= 0.316 Chirality : 0.042 0.246 1022 Planarity : 0.005 0.044 1100 Dihedral : 4.383 20.360 1004 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.92 % Allowed : 22.94 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.31), residues: 782 helix: 0.49 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -2.88 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.008 0.001 HIS A 205 PHE 0.022 0.001 PHE A 398 TYR 0.016 0.001 TYR B 336 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.777 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 119 average time/residue: 0.1470 time to fit residues: 24.7360 Evaluate side-chains 117 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0589 time to fit residues: 1.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4695 > 50: distance: 84 - 88: 3.550 distance: 88 - 89: 7.002 distance: 89 - 90: 11.298 distance: 89 - 92: 6.514 distance: 90 - 91: 16.497 distance: 90 - 93: 13.678 distance: 93 - 94: 8.413 distance: 93 - 99: 10.779 distance: 94 - 95: 10.901 distance: 94 - 97: 13.648 distance: 95 - 96: 13.743 distance: 95 - 100: 6.009 distance: 97 - 98: 7.787 distance: 98 - 99: 7.106 distance: 100 - 101: 6.846 distance: 101 - 102: 5.981 distance: 101 - 104: 3.612 distance: 102 - 103: 11.309 distance: 102 - 107: 7.630 distance: 104 - 105: 5.546 distance: 104 - 106: 12.688 distance: 107 - 108: 3.425 distance: 108 - 109: 6.243 distance: 108 - 111: 6.284 distance: 109 - 110: 18.710 distance: 109 - 115: 14.282 distance: 111 - 112: 8.860 distance: 112 - 113: 10.303 distance: 112 - 114: 6.028 distance: 115 - 116: 13.236 distance: 116 - 117: 9.880 distance: 116 - 119: 8.904 distance: 117 - 118: 34.027 distance: 117 - 123: 24.776 distance: 119 - 120: 11.455 distance: 119 - 121: 10.697 distance: 120 - 122: 10.457 distance: 123 - 124: 7.505 distance: 124 - 125: 17.974 distance: 124 - 127: 5.635 distance: 125 - 126: 18.108 distance: 125 - 135: 8.229 distance: 127 - 128: 11.843 distance: 128 - 129: 6.451 distance: 128 - 130: 6.939 distance: 129 - 131: 5.357 distance: 130 - 132: 3.664 distance: 131 - 133: 4.317 distance: 133 - 134: 3.969 distance: 135 - 136: 8.055 distance: 136 - 137: 8.958 distance: 136 - 139: 11.707 distance: 137 - 138: 9.689 distance: 137 - 140: 13.474 distance: 140 - 141: 3.683 distance: 141 - 142: 12.433 distance: 141 - 144: 13.909 distance: 142 - 143: 12.152 distance: 142 - 145: 8.629 distance: 147 - 148: 10.119 distance: 149 - 150: 3.902 distance: 151 - 152: 3.062 distance: 152 - 153: 3.618 distance: 152 - 155: 5.239 distance: 153 - 154: 6.350 distance: 153 - 163: 4.476 distance: 155 - 156: 4.934 distance: 156 - 158: 6.191 distance: 158 - 160: 4.277 distance: 159 - 161: 4.138 distance: 160 - 161: 5.524 distance: 161 - 162: 7.652 distance: 179 - 183: 3.410