Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:22:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2022/7cah_30331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2022/7cah_30331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2022/7cah_30331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2022/7cah_30331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2022/7cah_30331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cah_30331/12_2022/7cah_30331.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.212 sd= 3.720 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 2889 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1282 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 2.32, per 1000 atoms: 0.80 Number of scatterers: 2889 At special positions: 0 Unit cell: (68.64, 72.8, 64.48, 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 7 16.00 O 567 8.00 N 473 7.00 C 1842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 461.9 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 11.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.717A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.618A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.741A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.748A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 96 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 923 1.34 - 1.46: 741 1.46 - 1.58: 1294 1.58 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 2965 Sorted by residual: bond pdb=" C ILE E 51 " pdb=" N ASP E 52 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.47e-02 4.63e+03 1.73e+01 bond pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C THR A 430 " pdb=" N GLY A 431 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.13e-02 7.83e+03 8.60e-01 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.19e-02 7.06e+03 8.56e-01 bond pdb=" CB TRP D 93 " pdb=" CG TRP D 93 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.43e-01 ... (remaining 2960 not shown) Histogram of bond angle deviations from ideal: 102.35 - 109.77: 448 109.77 - 117.19: 1658 117.19 - 124.60: 1897 124.60 - 132.02: 53 132.02 - 139.44: 8 Bond angle restraints: 4064 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS A 378 " pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 123.00 118.23 4.77 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C LYS E 12 " pdb=" N LYS E 13 " pdb=" CA LYS E 13 " ideal model delta sigma weight residual 120.81 139.44 -18.63 5.77e+00 3.00e-02 1.04e+01 angle pdb=" C ILE E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta sigma weight residual 120.68 115.86 4.82 1.52e+00 4.33e-01 1.00e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.09 109.34 4.75 1.55e+00 4.16e-01 9.40e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1503 15.51 - 31.02: 170 31.02 - 46.53: 33 46.53 - 62.04: 1 62.04 - 77.55: 3 Dihedral angle restraints: 1710 sinusoidal: 535 harmonic: 1175 Sorted by residual: dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " pdb=" CA PRO E 103 " ideal model delta harmonic sigma weight residual -180.00 -137.55 -42.45 0 5.00e+00 4.00e-02 7.21e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 1707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 259 0.033 - 0.065: 116 0.065 - 0.098: 48 0.098 - 0.131: 23 0.131 - 0.163: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 450 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO E 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 412 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 3052 3.24 - 3.79: 4383 3.79 - 4.35: 5694 4.35 - 4.90: 9144 Nonbonded interactions: 22400 Sorted by model distance: nonbonded pdb=" OG SER E 119 " pdb=" O ALA E 121 " model vdw 2.137 2.440 nonbonded pdb=" O ASP E 102 " pdb=" N TYR E 104 " model vdw 2.222 2.520 nonbonded pdb=" OD2 ASP E 60 " pdb=" NZ LYS E 65 " model vdw 2.242 2.520 nonbonded pdb=" OD1 ASN A 437 " pdb=" N SER A 438 " model vdw 2.297 2.520 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.336 2.440 ... (remaining 22395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 1842 2.51 5 N 473 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.360 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: 1.840 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 13.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 2965 Z= 0.316 Angle : 0.921 18.632 4064 Z= 0.508 Chirality : 0.050 0.163 453 Planarity : 0.006 0.062 531 Dihedral : 13.676 77.553 951 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.95 % Favored : 79.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.53 % 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: -5.76 (0.31), residues: 396 helix: -4.70 (0.25), residues: 39 sheet: -3.12 (0.39), residues: 117 loop : -4.25 (0.30), residues: 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1144 time to fit residues: 6.3893 Evaluate side-chains 24 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 2965 Z= 0.186 Angle : 0.713 15.934 4064 Z= 0.359 Chirality : 0.048 0.187 453 Planarity : 0.006 0.059 531 Dihedral : 6.787 41.103 430 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.83 (0.34), residues: 396 helix: -3.88 (0.59), residues: 33 sheet: -2.56 (0.40), residues: 119 loop : -3.63 (0.33), residues: 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1019 time to fit residues: 5.9190 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0293 time to fit residues: 0.7409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 2965 Z= 0.225 Angle : 0.712 15.606 4064 Z= 0.362 Chirality : 0.047 0.142 453 Planarity : 0.006 0.059 531 Dihedral : 6.777 39.006 430 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.26 % 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: -4.58 (0.36), residues: 396 helix: -3.47 (0.56), residues: 39 sheet: -2.44 (0.41), residues: 120 loop : -3.45 (0.35), residues: 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.348 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 37 average time/residue: 0.1236 time to fit residues: 6.0194 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0319 time to fit residues: 0.6869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 2965 Z= 0.451 Angle : 0.871 18.767 4064 Z= 0.447 Chirality : 0.051 0.150 453 Planarity : 0.007 0.067 531 Dihedral : 7.774 40.323 430 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 21.21 % Favored : 78.54 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.87 (0.35), residues: 396 helix: -3.88 (0.52), residues: 33 sheet: -2.66 (0.40), residues: 122 loop : -3.62 (0.34), residues: 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.377 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 37 average time/residue: 0.1046 time to fit residues: 5.2743 Evaluate side-chains 33 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0310 time to fit residues: 0.7639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2965 Z= 0.227 Angle : 0.718 16.578 4064 Z= 0.363 Chirality : 0.047 0.141 453 Planarity : 0.006 0.061 531 Dihedral : 6.801 40.769 430 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.51 (0.36), residues: 396 helix: -3.68 (0.50), residues: 33 sheet: -2.31 (0.42), residues: 120 loop : -3.43 (0.35), residues: 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.351 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.1108 time to fit residues: 4.8835 Evaluate side-chains 29 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0307 time to fit residues: 0.5429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2965 Z= 0.238 Angle : 0.716 16.135 4064 Z= 0.363 Chirality : 0.047 0.140 453 Planarity : 0.006 0.060 531 Dihedral : 6.679 38.268 430 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.69 % Favored : 81.31 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.35 (0.38), residues: 396 helix: -3.64 (0.52), residues: 33 sheet: -2.21 (0.43), residues: 121 loop : -3.29 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.347 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 35 average time/residue: 0.1223 time to fit residues: 5.6695 Evaluate side-chains 29 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0297 time to fit residues: 0.4944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2965 Z= 0.268 Angle : 0.733 16.527 4064 Z= 0.373 Chirality : 0.047 0.167 453 Planarity : 0.006 0.061 531 Dihedral : 6.771 37.942 430 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % Favored : 82.32 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.31 (0.37), residues: 396 helix: -3.63 (0.52), residues: 33 sheet: -2.15 (0.43), residues: 121 loop : -3.28 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.350 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 0.1056 time to fit residues: 5.3182 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0297 time to fit residues: 0.5324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.0070 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 2965 Z= 0.236 Angle : 0.717 16.337 4064 Z= 0.364 Chirality : 0.047 0.181 453 Planarity : 0.006 0.058 531 Dihedral : 6.534 37.176 430 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 (0.38), residues: 396 helix: -3.53 (0.55), residues: 33 sheet: -2.06 (0.44), residues: 121 loop : -3.29 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.253 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 35 average time/residue: 0.0842 time to fit residues: 3.9964 Evaluate side-chains 32 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0254 time to fit residues: 0.4111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.0970 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.0060 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 2965 Z= 0.221 Angle : 0.703 15.981 4064 Z= 0.357 Chirality : 0.047 0.186 453 Planarity : 0.006 0.059 531 Dihedral : 6.383 36.017 430 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.17 (0.38), residues: 396 helix: -3.56 (0.49), residues: 39 sheet: -1.94 (0.44), residues: 120 loop : -3.21 (0.38), residues: 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.295 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.1111 time to fit residues: 4.9493 Evaluate side-chains 28 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2965 Z= 0.188 Angle : 0.689 16.539 4064 Z= 0.346 Chirality : 0.046 0.190 453 Planarity : 0.006 0.056 531 Dihedral : 6.130 34.910 430 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.95 (0.39), residues: 396 helix: -3.41 (0.54), residues: 39 sheet: -1.81 (0.45), residues: 119 loop : -3.06 (0.39), residues: 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.335 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1234 time to fit residues: 5.5361 Evaluate side-chains 29 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0299 time to fit residues: 0.5047 ------------------------------------------------------------------------------- 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-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 69.7517 > 50: distance: 92 - 95: 27.700 distance: 95 - 96: 14.167 distance: 96 - 97: 37.969 distance: 96 - 99: 17.130 distance: 97 - 101: 11.247 distance: 99 - 100: 20.346 distance: 101 - 102: 7.326 distance: 102 - 103: 31.233 distance: 102 - 105: 38.527 distance: 103 - 104: 56.572 distance: 103 - 112: 33.441 distance: 105 - 106: 25.397 distance: 106 - 107: 15.144 distance: 106 - 108: 18.352 distance: 107 - 109: 16.753 distance: 108 - 110: 27.405 distance: 109 - 111: 38.442 distance: 110 - 111: 32.952 distance: 112 - 113: 19.634 distance: 113 - 114: 40.951 distance: 113 - 116: 46.816 distance: 114 - 118: 24.903 distance: 116 - 117: 39.868 distance: 118 - 119: 29.353 distance: 118 - 239: 23.569 distance: 119 - 120: 22.400 distance: 119 - 122: 44.456 distance: 120 - 121: 7.075 distance: 120 - 125: 50.513 distance: 121 - 236: 31.638 distance: 122 - 123: 28.624 distance: 122 - 124: 26.980 distance: 125 - 126: 22.977 distance: 126 - 127: 22.689 distance: 126 - 129: 28.693 distance: 127 - 128: 15.324 distance: 127 - 136: 25.708 distance: 129 - 130: 22.365 distance: 130 - 131: 12.619 distance: 130 - 132: 20.635 distance: 131 - 133: 20.389 distance: 132 - 134: 31.946 distance: 133 - 135: 48.333 distance: 134 - 135: 48.572 distance: 136 - 225: 36.183 distance: 137 - 140: 33.248 distance: 138 - 139: 9.929 distance: 138 - 145: 28.281 distance: 139 - 222: 32.089 distance: 140 - 141: 15.003 distance: 141 - 142: 27.266 distance: 142 - 143: 24.292 distance: 143 - 144: 10.164 distance: 145 - 146: 45.143 distance: 146 - 147: 5.420 distance: 146 - 149: 17.807 distance: 147 - 148: 14.332 distance: 147 - 151: 45.015 distance: 149 - 150: 55.580 distance: 150 - 221: 24.328 distance: 151 - 152: 39.896 distance: 152 - 153: 33.997 distance: 153 - 154: 35.951 distance: 153 - 163: 34.132 distance: 155 - 156: 39.433 distance: 156 - 157: 56.726 distance: 156 - 158: 40.842 distance: 157 - 159: 55.432 distance: 159 - 161: 8.903 distance: 160 - 161: 30.771 distance: 161 - 162: 42.376 distance: 163 - 164: 39.680 distance: 164 - 165: 44.954 distance: 165 - 166: 37.409 distance: 165 - 167: 40.869 distance: 167 - 168: 9.722 distance: 168 - 169: 38.358 distance: 168 - 171: 28.121 distance: 169 - 170: 53.362 distance: 169 - 174: 32.374 distance: 171 - 172: 35.643 distance: 171 - 173: 11.256 distance: 177 - 189: 3.151