Starting phenix.real_space_refine on Sun Mar 10 19:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eya_31380/03_2024/7eya_31380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eya_31380/03_2024/7eya_31380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eya_31380/03_2024/7eya_31380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eya_31380/03_2024/7eya_31380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eya_31380/03_2024/7eya_31380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eya_31380/03_2024/7eya_31380.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2970 2.51 5 N 756 2.21 5 O 885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4629 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.20, per 1000 atoms: 0.69 Number of scatterers: 4629 At special positions: 0 Unit cell: (73.03, 95.92, 98.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 885 8.00 N 756 7.00 C 2970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN N 165 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 965.8 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1066 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 9.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 390 removed outlier: 4.456A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.287A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU R 516 " --> pdb=" O ASN R 394 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.535A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.577A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.750A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 29 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 50 through 51 removed outlier: 4.109A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 84 through 85 removed outlier: 3.547A pdb=" N SER N 172 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 224 through 229 removed outlier: 5.988A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL N 227 " --> pdb=" O ILE N 203 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 730 1.25 - 1.40: 1345 1.40 - 1.55: 2650 1.55 - 1.70: 1 1.70 - 1.84: 23 Bond restraints: 4749 Sorted by residual: bond pdb=" CG PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 1.503 1.107 0.396 3.40e-02 8.65e+02 1.36e+02 bond pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 1.492 1.155 0.337 5.00e-02 4.00e+02 4.54e+01 bond pdb=" N PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.80e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" N PRO R 507 " pdb=" CA PRO R 507 " ideal model delta sigma weight residual 1.467 1.486 -0.019 1.21e-02 6.83e+03 2.55e+00 ... (remaining 4744 not shown) Histogram of bond angle deviations from ideal: 76.09 - 91.30: 2 91.30 - 106.50: 109 106.50 - 121.70: 5167 121.70 - 136.90: 1165 136.90 - 152.10: 1 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N PRO R 507 " pdb=" CD PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 103.20 76.09 27.11 1.50e+00 4.44e-01 3.27e+02 angle pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 106.10 152.10 -46.00 3.20e+00 9.77e-02 2.07e+02 angle pdb=" CA PRO R 507 " pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 104.50 79.51 24.99 1.90e+00 2.77e-01 1.73e+02 angle pdb=" CA PRO R 507 " pdb=" N PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 112.00 102.91 9.09 1.40e+00 5.10e-01 4.22e+01 angle pdb=" C ASN N 165 " pdb=" CA ASN N 165 " pdb=" CB ASN N 165 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.17: 2587 22.17 - 44.34: 160 44.34 - 66.50: 21 66.50 - 88.67: 13 88.67 - 110.84: 12 Dihedral angle restraints: 2793 sinusoidal: 1120 harmonic: 1673 Sorted by residual: dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 134.96 45.04 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 164.63 -71.63 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 140.26 39.74 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 2790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 584 0.054 - 0.109: 90 0.109 - 0.163: 21 0.163 - 0.217: 1 0.217 - 0.272: 1 Chirality restraints: 697 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA CYS N 166 " pdb=" N CYS N 166 " pdb=" C CYS N 166 " pdb=" CB CYS N 166 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB VAL H 64 " pdb=" CA VAL H 64 " pdb=" CG1 VAL H 64 " pdb=" CG2 VAL H 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 694 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 506 " 0.057 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 507 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 507 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 507 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR N 38 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO N 39 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO N 39 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 39 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO L 95 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.037 5.00e-02 4.00e+02 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 122 2.69 - 3.24: 4233 3.24 - 3.80: 6527 3.80 - 4.35: 8655 4.35 - 4.90: 14738 Nonbonded interactions: 34275 Sorted by model distance: nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.142 2.440 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.187 2.440 nonbonded pdb=" O GLN H 3 " pdb=" OG SER H 25 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASN R 439 " pdb=" OG SER R 443 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.232 2.440 ... (remaining 34270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.000 Extract box with map and model: 13.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.008 0.396 4749 Z= 0.525 Angle : 1.005 46.004 6444 Z= 0.497 Chirality : 0.043 0.272 697 Planarity : 0.006 0.080 819 Dihedral : 16.975 110.839 1709 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.30 (0.35), residues: 554 helix: -2.80 (0.87), residues: 25 sheet: -0.56 (0.40), residues: 186 loop : -2.09 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS H 59 PHE 0.013 0.001 PHE R 456 TYR 0.023 0.001 TYR H 102 ARG 0.004 0.000 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.559 Fit side-chains REVERT: R 438 SER cc_start: 0.8217 (p) cc_final: 0.7686 (p) REVERT: H 83 MET cc_start: 0.6305 (ptt) cc_final: 0.6073 (ptt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1445 time to fit residues: 21.8590 Evaluate side-chains 94 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4749 Z= 0.195 Angle : 0.644 9.086 6444 Z= 0.334 Chirality : 0.044 0.235 697 Planarity : 0.006 0.069 819 Dihedral : 12.740 87.426 694 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 1.00 % Allowed : 10.16 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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 (0.35), residues: 554 helix: -2.54 (1.13), residues: 19 sheet: -0.36 (0.40), residues: 182 loop : -2.00 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS H 59 PHE 0.024 0.002 PHE R 429 TYR 0.015 0.001 TYR R 380 ARG 0.009 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.520 Fit side-chains REVERT: R 418 ILE cc_start: 0.9038 (tt) cc_final: 0.8714 (tt) REVERT: R 438 SER cc_start: 0.8176 (p) cc_final: 0.7632 (p) REVERT: R 465 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7698 (tm-30) outliers start: 5 outliers final: 3 residues processed: 105 average time/residue: 0.1508 time to fit residues: 20.6306 Evaluate side-chains 97 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 38 optimal weight: 0.0050 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 498 GLN H 3 GLN H 35 ASN N 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4749 Z= 0.163 Angle : 0.615 9.056 6444 Z= 0.313 Chirality : 0.045 0.255 697 Planarity : 0.005 0.066 819 Dihedral : 10.925 79.922 694 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.50 % Favored : 93.32 % Rotamer: Outliers : 0.80 % Allowed : 14.74 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.36), residues: 554 helix: -1.91 (1.61), residues: 13 sheet: -0.27 (0.40), residues: 184 loop : -1.92 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS H 59 PHE 0.034 0.002 PHE R 456 TYR 0.015 0.001 TYR R 380 ARG 0.005 0.001 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.516 Fit side-chains REVERT: R 418 ILE cc_start: 0.9146 (tt) cc_final: 0.8866 (tt) REVERT: R 438 SER cc_start: 0.8151 (p) cc_final: 0.7667 (p) REVERT: H 19 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7666 (mtp85) outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.1587 time to fit residues: 20.8058 Evaluate side-chains 99 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN L 96 HIS H 3 GLN H 35 ASN H 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4749 Z= 0.303 Angle : 0.679 9.265 6444 Z= 0.349 Chirality : 0.046 0.260 697 Planarity : 0.006 0.071 819 Dihedral : 9.842 71.439 694 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.03 % Favored : 90.79 % Rotamer: Outliers : 1.59 % Allowed : 16.93 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.02 (0.36), residues: 554 helix: -1.63 (1.57), residues: 13 sheet: -0.31 (0.39), residues: 193 loop : -2.05 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 353 HIS 0.001 0.000 HIS H 59 PHE 0.026 0.002 PHE N 43 TYR 0.022 0.002 TYR H 95 ARG 0.005 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.469 Fit side-chains REVERT: R 418 ILE cc_start: 0.9210 (tt) cc_final: 0.8966 (tt) REVERT: R 438 SER cc_start: 0.8146 (p) cc_final: 0.7627 (p) REVERT: H 19 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7561 (mtp85) REVERT: N 169 GLU cc_start: 0.7636 (mp0) cc_final: 0.7158 (mp0) outliers start: 8 outliers final: 8 residues processed: 101 average time/residue: 0.1643 time to fit residues: 21.3511 Evaluate side-chains 100 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4749 Z= 0.189 Angle : 0.648 11.895 6444 Z= 0.322 Chirality : 0.045 0.281 697 Planarity : 0.005 0.065 819 Dihedral : 8.872 62.729 694 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 2.19 % Allowed : 17.53 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.36), residues: 554 helix: -1.46 (1.54), residues: 13 sheet: -0.43 (0.38), residues: 201 loop : -2.00 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 353 HIS 0.001 0.000 HIS L 96 PHE 0.020 0.001 PHE N 43 TYR 0.013 0.001 TYR H 95 ARG 0.004 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.548 Fit side-chains REVERT: R 438 SER cc_start: 0.7842 (p) cc_final: 0.7318 (p) REVERT: H 19 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7562 (mtp85) REVERT: N 58 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: N 169 GLU cc_start: 0.7524 (mp0) cc_final: 0.7076 (mp0) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.1526 time to fit residues: 20.2387 Evaluate side-chains 99 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4749 Z= 0.216 Angle : 0.653 12.842 6444 Z= 0.325 Chirality : 0.044 0.261 697 Planarity : 0.005 0.069 819 Dihedral : 7.911 51.393 694 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.48 % Favored : 91.34 % Rotamer: Outliers : 2.79 % Allowed : 18.13 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.36), residues: 554 helix: -1.18 (1.53), residues: 13 sheet: -0.39 (0.38), residues: 200 loop : -1.99 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 353 HIS 0.001 0.000 HIS L 96 PHE 0.022 0.002 PHE N 43 TYR 0.016 0.001 TYR H 95 ARG 0.003 0.001 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.544 Fit side-chains REVERT: R 438 SER cc_start: 0.7827 (p) cc_final: 0.7307 (p) REVERT: H 19 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7497 (mtp85) REVERT: H 121 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.5710 (pm20) REVERT: N 32 PHE cc_start: 0.8128 (p90) cc_final: 0.7833 (p90) REVERT: N 58 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: N 169 GLU cc_start: 0.7533 (mp0) cc_final: 0.7041 (mp0) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.1660 time to fit residues: 21.6508 Evaluate side-chains 104 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4749 Z= 0.203 Angle : 0.638 9.833 6444 Z= 0.320 Chirality : 0.044 0.200 697 Planarity : 0.005 0.065 819 Dihedral : 6.673 45.241 694 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Rotamer: Outliers : 2.79 % Allowed : 18.53 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.36), residues: 554 helix: -1.09 (1.55), residues: 13 sheet: -0.45 (0.38), residues: 206 loop : -1.95 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 353 HIS 0.003 0.001 HIS H 59 PHE 0.021 0.002 PHE N 43 TYR 0.014 0.001 TYR H 95 ARG 0.003 0.000 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.539 Fit side-chains REVERT: R 438 SER cc_start: 0.7835 (p) cc_final: 0.7347 (p) REVERT: H 19 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7460 (mtp85) REVERT: H 121 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.5783 (pm20) REVERT: N 32 PHE cc_start: 0.8073 (p90) cc_final: 0.7781 (p90) REVERT: N 58 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: N 169 GLU cc_start: 0.7554 (mp0) cc_final: 0.6985 (mp0) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.1453 time to fit residues: 18.7391 Evaluate side-chains 101 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4749 Z= 0.226 Angle : 0.639 9.126 6444 Z= 0.325 Chirality : 0.044 0.191 697 Planarity : 0.005 0.069 819 Dihedral : 5.594 45.338 694 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.03 % Favored : 90.79 % Rotamer: Outliers : 3.78 % Allowed : 18.33 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.36), residues: 554 helix: -1.05 (1.56), residues: 13 sheet: -0.43 (0.38), residues: 206 loop : -1.96 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 353 HIS 0.001 0.000 HIS H 59 PHE 0.024 0.002 PHE N 43 TYR 0.017 0.001 TYR H 95 ARG 0.003 0.000 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.523 Fit side-chains REVERT: R 438 SER cc_start: 0.7988 (p) cc_final: 0.7556 (p) REVERT: H 121 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.5749 (pm20) REVERT: N 58 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: N 169 GLU cc_start: 0.7533 (mp0) cc_final: 0.6941 (mp0) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.1375 time to fit residues: 18.6182 Evaluate side-chains 106 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 498 GLN Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1052 > 50: distance: 23 - 28: 20.799 distance: 28 - 29: 11.425 distance: 28 - 183: 20.926 distance: 29 - 30: 11.549 distance: 29 - 32: 14.925 distance: 30 - 31: 8.105 distance: 30 - 36: 23.810 distance: 31 - 180: 27.983 distance: 32 - 33: 22.056 distance: 33 - 34: 21.367 distance: 33 - 35: 16.656 distance: 36 - 37: 30.775 distance: 36 - 42: 26.000 distance: 37 - 38: 44.326 distance: 38 - 39: 3.747 distance: 38 - 43: 49.493 distance: 40 - 41: 20.327 distance: 41 - 42: 16.202 distance: 43 - 44: 48.901 distance: 44 - 45: 39.585 distance: 44 - 47: 26.942 distance: 45 - 46: 6.848 distance: 45 - 54: 37.307 distance: 47 - 48: 15.042 distance: 48 - 49: 9.233 distance: 49 - 51: 3.533 distance: 50 - 52: 7.004 distance: 51 - 53: 10.859 distance: 52 - 53: 4.607 distance: 54 - 55: 7.482 distance: 55 - 56: 34.072 distance: 55 - 58: 21.799 distance: 56 - 57: 10.056 distance: 56 - 62: 10.609 distance: 58 - 59: 9.543 distance: 59 - 61: 5.501 distance: 62 - 63: 31.198 distance: 63 - 64: 41.226 distance: 63 - 66: 12.408 distance: 64 - 65: 6.936 distance: 64 - 70: 13.737 distance: 66 - 67: 14.700 distance: 67 - 68: 11.657 distance: 67 - 69: 12.551 distance: 70 - 71: 9.229 distance: 71 - 72: 25.403 distance: 72 - 73: 32.405 distance: 72 - 74: 4.599 distance: 74 - 75: 25.879 distance: 74 - 150: 20.097 distance: 75 - 76: 26.682 distance: 75 - 78: 11.320 distance: 76 - 77: 13.656 distance: 76 - 81: 35.131 distance: 77 - 147: 30.757 distance: 78 - 79: 23.552 distance: 78 - 80: 16.188 distance: 81 - 82: 20.238 distance: 81 - 222: 23.255 distance: 82 - 83: 14.652 distance: 82 - 85: 25.053 distance: 83 - 84: 14.252 distance: 83 - 93: 17.096 distance: 84 - 219: 33.933 distance: 85 - 86: 15.407 distance: 86 - 87: 9.152 distance: 86 - 88: 4.467 distance: 87 - 89: 15.102 distance: 88 - 90: 14.636 distance: 90 - 91: 4.445 distance: 91 - 92: 11.356 distance: 93 - 94: 7.700 distance: 93 - 136: 5.158 distance: 94 - 95: 15.086 distance: 94 - 97: 11.016 distance: 95 - 96: 10.383 distance: 95 - 104: 27.561 distance: 96 - 133: 22.592 distance: 97 - 98: 11.119 distance: 98 - 99: 9.485 distance: 98 - 100: 17.830 distance: 99 - 101: 7.868 distance: 100 - 102: 5.253 distance: 101 - 103: 15.861 distance: 102 - 103: 20.498 distance: 104 - 105: 6.331 distance: 104 - 208: 14.354 distance: 105 - 106: 10.363 distance: 105 - 108: 18.686 distance: 106 - 107: 8.252 distance: 106 - 109: 8.075 distance: 107 - 205: 5.569