Starting phenix.real_space_refine on Fri Dec 27 12:33:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eya_31380/12_2024/7eya_31380.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eya_31380/12_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/cci-nas-00/data/ceres_data/7eya_31380/12_2024/7eya_31380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eya_31380/12_2024/7eya_31380.map" model { file = "/net/cci-nas-00/data/ceres_data/7eya_31380/12_2024/7eya_31380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eya_31380/12_2024/7eya_31380.cif" } 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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.46, per 1000 atoms: 0.96 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 - 3.00 Amino acid : True - 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: 1.17 Conformation dependent library (CDL) restraints added in 600.4 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: 0.59 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: 1.26 Time building geometry restraints manager: 1.37 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: 0.00 - 9.20: 6441 9.20 - 18.40: 0 18.40 - 27.60: 2 27.60 - 36.80: 0 36.80 - 46.00: 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 3.040 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.187 3.040 nonbonded pdb=" O GLN H 3 " pdb=" OG SER H 25 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASN R 439 " pdb=" OG SER R 443 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.232 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.720 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.660 Find NCS groups from input model: 0.060 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.537 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: 0.1481 time to fit residues: 22.4789 Evaluate side-chains 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 chunk 22 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4749 Z= 0.189 Angle : 0.670 9.172 6444 Z= 0.347 Chirality : 0.045 0.249 697 Planarity : 0.006 0.068 819 Dihedral : 12.329 84.867 694 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 1.00 % Allowed : 9.36 % Favored : 89.64 % 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: -2.13 (0.35), residues: 554 helix: -2.99 (0.88), residues: 25 sheet: -0.32 (0.41), residues: 181 loop : -2.00 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 35 HIS 0.001 0.000 HIS H 59 PHE 0.026 0.002 PHE N 43 TYR 0.016 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 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.517 Fit side-chains REVERT: R 418 ILE cc_start: 0.9036 (tt) cc_final: 0.8757 (tt) REVERT: R 438 SER cc_start: 0.8091 (p) cc_final: 0.7569 (p) outliers start: 5 outliers final: 3 residues processed: 109 average time/residue: 0.1549 time to fit residues: 22.0819 Evaluate side-chains 100 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain L residue 97 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: 0.0970 chunk 15 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4749 Z= 0.159 Angle : 0.630 8.823 6444 Z= 0.321 Chirality : 0.045 0.265 697 Planarity : 0.005 0.066 819 Dihedral : 10.553 76.974 694 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 0.80 % Allowed : 13.55 % Favored : 85.66 % 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: -2.68 (1.19), residues: 19 sheet: -0.15 (0.40), residues: 186 loop : -1.98 (0.32), residues: 349 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 0.027 0.002 PHE R 456 TYR 0.017 0.001 TYR R 380 ARG 0.005 0.001 ARG H 100 *********************** 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 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.551 Fit side-chains REVERT: R 418 ILE cc_start: 0.9172 (tt) cc_final: 0.8947 (tt) REVERT: R 438 SER cc_start: 0.8079 (p) cc_final: 0.7680 (p) REVERT: H 19 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7451 (mtp85) REVERT: N 32 PHE cc_start: 0.8032 (p90) cc_final: 0.7704 (p90) outliers start: 4 outliers final: 3 residues processed: 105 average time/residue: 0.1565 time to fit residues: 21.2135 Evaluate side-chains 99 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 H 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 4749 Z= 0.426 Angle : 0.762 12.293 6444 Z= 0.395 Chirality : 0.049 0.256 697 Planarity : 0.007 0.077 819 Dihedral : 9.995 70.284 694 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.93 % Favored : 89.89 % Rotamer: Outliers : 2.39 % Allowed : 15.94 % Favored : 81.67 % 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: -2.28 (0.36), residues: 554 helix: -2.88 (0.97), residues: 21 sheet: -0.58 (0.39), residues: 197 loop : -2.10 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 353 HIS 0.003 0.001 HIS H 59 PHE 0.038 0.003 PHE R 456 TYR 0.028 0.002 TYR H 95 ARG 0.004 0.001 ARG H 98 *********************** 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 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.534 Fit side-chains REVERT: R 355 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7526 (ttt90) REVERT: R 418 ILE cc_start: 0.9216 (tt) cc_final: 0.8992 (tt) REVERT: R 438 SER cc_start: 0.8261 (p) cc_final: 0.7671 (p) REVERT: R 508 TYR cc_start: 0.8414 (m-10) cc_final: 0.8149 (m-10) REVERT: H 19 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7613 (mtp85) REVERT: N 58 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7837 (m-10) REVERT: N 169 GLU cc_start: 0.7676 (mp0) cc_final: 0.7155 (mp0) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.1650 time to fit residues: 22.4380 Evaluate side-chains 104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain N residue 58 PHE 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: 0.5980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4749 Z= 0.171 Angle : 0.640 8.809 6444 Z= 0.326 Chirality : 0.045 0.270 697 Planarity : 0.005 0.065 819 Dihedral : 9.094 64.865 694 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 1.99 % Allowed : 16.73 % Favored : 81.27 % 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: -2.20 (0.36), residues: 554 helix: -2.90 (0.86), residues: 27 sheet: -0.45 (0.39), residues: 200 loop : -2.08 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 3 HIS 0.002 0.001 HIS H 59 PHE 0.022 0.001 PHE N 43 TYR 0.012 0.001 TYR R 380 ARG 0.003 0.001 ARG R 408 *********************** 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 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.536 Fit side-chains REVERT: R 355 ARG cc_start: 0.7710 (ttt90) cc_final: 0.7383 (ttt180) REVERT: R 438 SER cc_start: 0.8172 (p) cc_final: 0.7619 (p) REVERT: L 36 TYR cc_start: 0.8854 (m-80) cc_final: 0.8645 (m-80) REVERT: H 19 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7576 (mtp85) REVERT: N 169 GLU cc_start: 0.7543 (mp0) cc_final: 0.7111 (mp0) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.1459 time to fit residues: 19.5692 Evaluate side-chains 100 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4749 Z= 0.197 Angle : 0.633 9.045 6444 Z= 0.323 Chirality : 0.045 0.251 697 Planarity : 0.005 0.070 819 Dihedral : 8.398 58.042 694 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.94 % Favored : 91.88 % Rotamer: Outliers : 2.59 % Allowed : 17.13 % 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: -2.06 (0.36), residues: 554 helix: -2.24 (1.15), residues: 19 sheet: -0.48 (0.39), residues: 207 loop : -1.98 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 3 HIS 0.001 0.000 HIS L 96 PHE 0.027 0.002 PHE R 456 TYR 0.014 0.001 TYR H 95 ARG 0.003 0.000 ARG R 408 *********************** 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 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.544 Fit side-chains REVERT: R 406 GLU cc_start: 0.8402 (pm20) cc_final: 0.8148 (pm20) REVERT: R 438 SER cc_start: 0.7839 (p) cc_final: 0.7274 (p) REVERT: H 121 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.5670 (pm20) REVERT: N 169 GLU cc_start: 0.7549 (mp0) cc_final: 0.6999 (mp0) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.1464 time to fit residues: 19.4360 Evaluate side-chains 104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 121 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4749 Z= 0.218 Angle : 0.641 9.422 6444 Z= 0.327 Chirality : 0.044 0.235 697 Planarity : 0.005 0.066 819 Dihedral : 7.760 50.431 694 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 3.19 % Allowed : 16.93 % Favored : 79.88 % 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: -2.05 (0.36), residues: 554 helix: -2.73 (0.89), residues: 27 sheet: -0.37 (0.39), residues: 205 loop : -1.98 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 3 HIS 0.000 0.000 HIS H 59 PHE 0.024 0.001 PHE N 43 TYR 0.015 0.001 TYR H 95 ARG 0.003 0.000 ARG H 100 *********************** 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 111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.537 Fit side-chains REVERT: R 406 GLU cc_start: 0.8412 (pm20) cc_final: 0.8164 (pm20) REVERT: R 438 SER cc_start: 0.7904 (p) cc_final: 0.7356 (p) REVERT: H 18 LEU cc_start: 0.7861 (tp) cc_final: 0.7629 (tt) REVERT: H 121 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.5667 (pm20) REVERT: N 58 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: N 169 GLU cc_start: 0.7572 (mp0) cc_final: 0.7008 (mp0) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.1571 time to fit residues: 21.0210 Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL 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 N residue 58 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4749 Z= 0.188 Angle : 0.634 9.214 6444 Z= 0.320 Chirality : 0.044 0.197 697 Planarity : 0.005 0.069 819 Dihedral : 6.697 44.972 694 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.30 % Favored : 91.52 % Rotamer: Outliers : 3.19 % Allowed : 17.33 % Favored : 79.48 % 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 (0.37), residues: 554 helix: -2.17 (1.14), residues: 19 sheet: -0.40 (0.39), residues: 207 loop : -1.89 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 353 HIS 0.000 0.000 HIS N 66 PHE 0.022 0.001 PHE N 43 TYR 0.013 0.001 TYR H 95 ARG 0.004 0.000 ARG R 408 *********************** 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 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.540 Fit side-chains REVERT: R 438 SER cc_start: 0.7805 (p) cc_final: 0.7264 (p) REVERT: L 36 TYR cc_start: 0.8820 (m-80) cc_final: 0.8609 (m-80) REVERT: H 121 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5738 (pm20) REVERT: N 58 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: N 169 GLU cc_start: 0.7539 (mp0) cc_final: 0.6954 (mp0) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.1363 time to fit residues: 18.4381 Evaluate side-chains 104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 58 VAL 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 N residue 58 PHE 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 ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4749 Z= 0.257 Angle : 0.661 8.144 6444 Z= 0.336 Chirality : 0.045 0.191 697 Planarity : 0.005 0.067 819 Dihedral : 6.001 46.193 694 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.94 % Favored : 91.88 % Rotamer: Outliers : 3.98 % Allowed : 17.13 % Favored : 78.88 % 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: -2.74 (0.87), residues: 27 sheet: -0.32 (0.39), residues: 202 loop : -1.97 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 353 HIS 0.001 0.000 HIS L 96 PHE 0.025 0.002 PHE N 43 TYR 0.018 0.001 TYR H 95 ARG 0.003 0.000 ARG R 408 *********************** REFINEMENT MACRO_CYCLE 9 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 111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.544 Fit side-chains REVERT: R 438 SER cc_start: 0.7910 (p) cc_final: 0.7357 (p) REVERT: H 121 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: N 58 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: N 169 GLU cc_start: 0.7547 (mp0) cc_final: 0.6947 (mp0) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.1564 time to fit residues: 21.1786 Evaluate side-chains 104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL 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 N residue 58 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 40 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2851 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= 0.197 Angle : 0.638 8.044 6444 Z= 0.326 Chirality : 0.044 0.191 697 Planarity : 0.005 0.066 819 Dihedral : 5.222 45.167 694 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.12 % Favored : 91.70 % Rotamer: Outliers : 3.19 % Allowed : 17.53 % Favored : 79.28 % 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: -1.95 (0.37), residues: 554 helix: -2.72 (0.88), residues: 27 sheet: -0.30 (0.39), residues: 205 loop : -1.91 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 353 HIS 0.000 0.000 HIS N 66 PHE 0.022 0.001 PHE N 43 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG R 408 ********************** REFINEMENT MACRO_CYCLE 10 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 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.530 Fit side-chains REVERT: R 438 SER cc_start: 0.7796 (p) cc_final: 0.7283 (p) REVERT: H 121 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.5739 (pm20) REVERT: N 58 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: N 169 GLU cc_start: 0.7519 (mp0) cc_final: 0.6929 (mp0) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.1567 time to fit residues: 20.9599 Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 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 N residue 58 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.158607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135469 restraints weight = 6523.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138249 restraints weight = 9110.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139458 restraints weight = 5508.695| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2959 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= 0.200 Angle : 0.638 8.059 6444 Z= 0.329 Chirality : 0.044 0.189 697 Planarity : 0.005 0.067 819 Dihedral : 5.181 45.411 694 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.30 % Favored : 91.52 % Rotamer: Outliers : 3.39 % Allowed : 17.73 % Favored : 78.88 % 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 (0.37), residues: 554 helix: -2.77 (0.87), residues: 27 sheet: -0.28 (0.38), residues: 205 loop : -1.92 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 353 HIS 0.000 0.000 HIS H 59 PHE 0.022 0.001 PHE N 43 TYR 0.014 0.001 TYR H 95 ARG 0.004 0.000 ARG R 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1538.78 seconds wall clock time: 28 minutes 27.89 seconds (1707.89 seconds total)