Starting phenix.real_space_refine on Thu Dec 7 17:30:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvl_34131/12_2023/7yvl_34131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvl_34131/12_2023/7yvl_34131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvl_34131/12_2023/7yvl_34131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvl_34131/12_2023/7yvl_34131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvl_34131/12_2023/7yvl_34131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvl_34131/12_2023/7yvl_34131.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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 14 5.16 5 C 2066 2.51 5 N 531 2.21 5 O 613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3224 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1511 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 2.11, per 1000 atoms: 0.65 Number of scatterers: 3224 At special positions: 0 Unit cell: (81.18, 71.34, 95.12, 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 14 16.00 O 613 8.00 N 531 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.12 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: 1.08 Conformation dependent library (CDL) restraints added in 556.6 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.801A pdb=" N THR A 92 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.601A pdb=" N ASP C 85 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.105A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.843A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.707A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.605A pdb=" N THR A 83 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 5.617A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 95 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 113 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.990A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.545A pdb=" N VAL C 99 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AA7, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 81 hydrogen bonds defined for protein. 174 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: 0.73 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 506 1.28 - 1.42: 949 1.42 - 1.56: 1839 1.56 - 1.71: 0 1.71 - 1.85: 16 Bond restraints: 3310 Sorted by residual: bond pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 1.331 1.533 -0.202 1.65e-02 3.67e+03 1.50e+02 bond pdb=" CA TYR C 93 " pdb=" C TYR C 93 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.26e-02 6.30e+03 9.99e+01 bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.242 1.161 0.081 8.60e-03 1.35e+04 8.86e+01 bond pdb=" C TYR C 93 " pdb=" O TYR C 93 " ideal model delta sigma weight residual 1.234 1.137 0.097 1.19e-02 7.06e+03 6.67e+01 bond pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 1.539 1.495 0.044 5.40e-03 3.43e+04 6.58e+01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.60: 67 104.60 - 112.07: 1561 112.07 - 119.54: 1118 119.54 - 127.01: 1728 127.01 - 134.47: 42 Bond angle restraints: 4516 Sorted by residual: angle pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 110.45 118.23 -7.78 7.80e-01 1.64e+00 9.95e+01 angle pdb=" O TYR C 38 " pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 123.27 134.47 -11.20 1.22e+00 6.72e-01 8.43e+01 angle pdb=" C TYR C 93 " pdb=" CA TYR C 93 " pdb=" CB TYR C 93 " ideal model delta sigma weight residual 109.72 97.13 12.59 1.66e+00 3.63e-01 5.75e+01 angle pdb=" CA TYR C 38 " pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 116.00 105.28 10.72 1.50e+00 4.44e-01 5.11e+01 angle pdb=" C SER C 97 " pdb=" CA SER C 97 " pdb=" CB SER C 97 " ideal model delta sigma weight residual 109.99 99.03 10.96 1.61e+00 3.86e-01 4.63e+01 ... (remaining 4511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1708 15.10 - 30.20: 180 30.20 - 45.29: 45 45.29 - 60.39: 9 60.39 - 75.49: 2 Dihedral angle restraints: 1944 sinusoidal: 727 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.49 -75.49 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta harmonic sigma weight residual 123.40 141.60 -18.20 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" C ILE A 102 " pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta harmonic sigma weight residual -122.00 -139.22 17.22 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 487 0.159 - 0.317: 13 0.317 - 0.476: 2 0.476 - 0.635: 0 0.635 - 0.793: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 1.64 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA SER C 96 " pdb=" N SER C 96 " pdb=" C SER C 96 " pdb=" CB SER C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR C 95 " pdb=" N THR C 95 " pdb=" C THR C 95 " pdb=" CB THR C 95 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 500 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A 103 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 485 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLY B 485 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 485 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL B 486 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 97 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C SER C 97 " -0.047 2.00e-02 2.50e+03 pdb=" O SER C 97 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 98 " 0.016 2.00e-02 2.50e+03 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 183 2.70 - 3.25: 3086 3.25 - 3.80: 4704 3.80 - 4.35: 6139 4.35 - 4.90: 10672 Nonbonded interactions: 24784 Sorted by model distance: nonbonded pdb=" O ASN B 388 " pdb=" OD1 ASN B 388 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.199 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 119 " model vdw 2.251 2.440 nonbonded pdb=" O ILE A 105 " pdb=" OH TYR C 38 " model vdw 2.307 2.440 nonbonded pdb=" O THR A 92 " pdb=" OG1 THR A 92 " model vdw 2.366 2.440 ... (remaining 24779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.460 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: 0.010 Extract box with map and model: 27.070 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 12.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.011 0.202 3310 Z= 0.661 Angle : 1.163 12.585 4516 Z= 0.730 Chirality : 0.075 0.793 503 Planarity : 0.007 0.098 574 Dihedral : 12.977 71.126 1154 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.96 % Favored : 90.56 % Rotamer: Outliers : 1.42 % Allowed : 15.95 % Favored : 82.62 % Cbeta Deviations : 1.30 % 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: -4.93 (0.33), residues: 413 helix: -4.88 (0.35), residues: 29 sheet: -2.71 (0.37), residues: 143 loop : -3.55 (0.32), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 55 HIS 0.008 0.002 HIS A 99 PHE 0.016 0.002 PHE A 106 TYR 0.020 0.002 TYR B 489 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.376 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 121 average time/residue: 0.2032 time to fit residues: 28.5951 Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0360 time to fit residues: 0.5870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN B 370 ASN B 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3310 Z= 0.231 Angle : 0.723 13.899 4516 Z= 0.352 Chirality : 0.045 0.172 503 Planarity : 0.004 0.031 574 Dihedral : 4.725 24.904 460 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 5.13 % Allowed : 20.80 % Favored : 74.07 % 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: -3.74 (0.35), residues: 413 helix: -4.60 (0.57), residues: 22 sheet: -1.77 (0.40), residues: 145 loop : -2.84 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.001 0.001 HIS A 99 PHE 0.008 0.001 PHE B 400 TYR 0.019 0.001 TYR C 93 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 98 average time/residue: 0.1576 time to fit residues: 18.6412 Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0349 time to fit residues: 1.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3310 Z= 0.185 Angle : 0.615 9.961 4516 Z= 0.313 Chirality : 0.044 0.152 503 Planarity : 0.004 0.029 574 Dihedral : 4.356 22.453 460 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 3.42 % Allowed : 24.22 % Favored : 72.36 % 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: -3.12 (0.36), residues: 413 helix: -4.86 (0.34), residues: 20 sheet: -1.18 (0.40), residues: 148 loop : -2.49 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 49 HIS 0.002 0.001 HIS B 519 PHE 0.010 0.001 PHE B 342 TYR 0.013 0.001 TYR C 93 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.384 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 0.1558 time to fit residues: 15.8489 Evaluate side-chains 74 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0348 time to fit residues: 0.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3310 Z= 0.283 Angle : 0.683 10.087 4516 Z= 0.350 Chirality : 0.045 0.151 503 Planarity : 0.004 0.033 574 Dihedral : 4.932 25.475 460 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.47 % Favored : 91.28 % Rotamer: Outliers : 6.27 % Allowed : 24.50 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.36), residues: 413 helix: -4.97 (0.23), residues: 21 sheet: -0.58 (0.41), residues: 138 loop : -2.54 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 109 HIS 0.003 0.001 HIS A 99 PHE 0.008 0.002 PHE B 347 TYR 0.014 0.001 TYR C 93 ARG 0.002 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 93 average time/residue: 0.1681 time to fit residues: 18.7191 Evaluate side-chains 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0362 time to fit residues: 1.3087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7867 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3310 Z= 0.214 Angle : 0.669 10.033 4516 Z= 0.344 Chirality : 0.045 0.146 503 Planarity : 0.004 0.031 574 Dihedral : 4.840 24.167 460 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 3.70 % Allowed : 24.22 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.37), residues: 413 helix: -5.00 (0.22), residues: 19 sheet: -0.44 (0.42), residues: 140 loop : -2.43 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 PHE 0.009 0.001 PHE B 400 TYR 0.011 0.001 TYR C 93 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 0.1611 time to fit residues: 16.3341 Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.325 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0351 time to fit residues: 0.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3310 Z= 0.229 Angle : 0.654 9.151 4516 Z= 0.333 Chirality : 0.045 0.157 503 Planarity : 0.004 0.032 574 Dihedral : 4.757 21.097 460 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.23 % Favored : 91.53 % Rotamer: Outliers : 1.42 % Allowed : 26.78 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.37), residues: 413 helix: -4.98 (0.22), residues: 21 sheet: -0.26 (0.43), residues: 138 loop : -2.34 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 PHE 0.011 0.001 PHE A 24 TYR 0.012 0.001 TYR C 93 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.379 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.1615 time to fit residues: 15.3230 Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1028 time to fit residues: 1.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN C 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3310 Z= 0.223 Angle : 0.660 10.692 4516 Z= 0.330 Chirality : 0.045 0.176 503 Planarity : 0.004 0.034 574 Dihedral : 4.736 20.848 460 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.75 % Favored : 92.01 % Rotamer: Outliers : 1.14 % Allowed : 26.78 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.38), residues: 413 helix: -4.98 (0.23), residues: 19 sheet: -0.11 (0.44), residues: 136 loop : -2.23 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.009 0.001 PHE A 24 TYR 0.014 0.001 TYR C 93 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.1547 time to fit residues: 14.0057 Evaluate side-chains 74 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0316 time to fit residues: 0.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3310 Z= 0.218 Angle : 0.657 10.396 4516 Z= 0.328 Chirality : 0.044 0.157 503 Planarity : 0.004 0.048 574 Dihedral : 4.715 18.913 460 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.72 % Favored : 91.04 % Rotamer: Outliers : 0.57 % Allowed : 29.63 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.38), residues: 413 helix: -4.99 (0.22), residues: 21 sheet: -0.10 (0.44), residues: 136 loop : -2.13 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.010 0.001 PHE B 400 TYR 0.013 0.001 TYR C 93 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.403 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.1769 time to fit residues: 14.9467 Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0364 time to fit residues: 0.6505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3310 Z= 0.230 Angle : 0.662 9.616 4516 Z= 0.331 Chirality : 0.045 0.187 503 Planarity : 0.004 0.052 574 Dihedral : 4.873 21.283 460 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.72 % Favored : 91.04 % Rotamer: Outliers : 0.85 % Allowed : 29.34 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.38), residues: 413 helix: -4.98 (0.22), residues: 21 sheet: -0.07 (0.44), residues: 136 loop : -2.00 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 109 HIS 0.002 0.001 HIS A 99 PHE 0.009 0.001 PHE A 24 TYR 0.013 0.001 TYR C 93 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.1664 time to fit residues: 14.1914 Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0448 time to fit residues: 0.5878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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: 0.7903 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3310 Z= 0.185 Angle : 0.650 9.063 4516 Z= 0.321 Chirality : 0.044 0.178 503 Planarity : 0.004 0.046 574 Dihedral : 4.713 22.490 460 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.96 % Favored : 90.80 % Rotamer: Outliers : 0.57 % Allowed : 29.34 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.38), residues: 413 helix: -4.97 (0.22), residues: 21 sheet: 0.04 (0.44), residues: 135 loop : -1.99 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.008 0.001 PHE B 400 TYR 0.017 0.001 TYR A 108 ARG 0.002 0.000 ARG C 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.1628 time to fit residues: 13.8344 Evaluate side-chains 64 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0366 time to fit residues: 0.5162 ------------------------------------------------------------------------------- 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: 64.5979 > 50: distance: 47 - 101: 31.956 distance: 50 - 98: 11.812 distance: 69 - 93: 25.373 distance: 72 - 90: 24.147 distance: 85 - 90: 23.733 distance: 91 - 92: 13.808 distance: 91 - 94: 13.358 distance: 92 - 93: 7.301 distance: 92 - 98: 32.202 distance: 94 - 95: 12.272 distance: 95 - 96: 13.500 distance: 95 - 97: 32.912 distance: 98 - 99: 28.656 distance: 99 - 100: 14.904 distance: 99 - 102: 27.163 distance: 100 - 101: 31.723 distance: 100 - 104: 15.484 distance: 102 - 103: 34.662 distance: 104 - 105: 39.218 distance: 105 - 106: 22.699 distance: 105 - 108: 28.586 distance: 106 - 107: 28.097 distance: 106 - 115: 25.854 distance: 108 - 109: 16.360 distance: 109 - 110: 8.627 distance: 109 - 111: 15.346 distance: 110 - 112: 14.769 distance: 111 - 113: 13.448 distance: 112 - 114: 27.315 distance: 113 - 114: 20.984 distance: 115 - 116: 24.502 distance: 116 - 117: 45.005 distance: 116 - 119: 13.864 distance: 117 - 118: 20.321 distance: 117 - 120: 42.158 distance: 120 - 121: 18.302 distance: 121 - 122: 7.549 distance: 121 - 124: 32.027 distance: 122 - 123: 8.898 distance: 122 - 128: 18.490 distance: 124 - 125: 28.978 distance: 125 - 126: 11.354 distance: 125 - 127: 40.421 distance: 128 - 129: 3.198 distance: 129 - 130: 17.398 distance: 129 - 132: 7.075 distance: 130 - 131: 8.726 distance: 130 - 136: 22.182 distance: 132 - 133: 6.966 distance: 133 - 134: 13.586 distance: 133 - 135: 24.859 distance: 136 - 137: 30.728 distance: 137 - 138: 31.427 distance: 137 - 140: 21.006 distance: 138 - 139: 22.871 distance: 138 - 146: 22.853 distance: 140 - 141: 24.549 distance: 141 - 142: 11.958 distance: 141 - 143: 26.190 distance: 142 - 144: 7.467 distance: 143 - 145: 4.909 distance: 144 - 145: 27.870 distance: 146 - 147: 6.735 distance: 147 - 148: 36.855 distance: 147 - 150: 8.986 distance: 148 - 149: 42.735 distance: 148 - 151: 26.868 distance: 151 - 152: 8.294 distance: 151 - 157: 33.111 distance: 152 - 153: 39.378 distance: 152 - 155: 32.212 distance: 153 - 154: 11.793 distance: 153 - 158: 11.143 distance: 156 - 157: 25.989 distance: 158 - 159: 35.056 distance: 159 - 160: 15.997 distance: 159 - 162: 7.975 distance: 160 - 161: 8.665 distance: 160 - 163: 23.640