Starting phenix.real_space_refine on Sun Mar 10 17:52:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/03_2024/8csv_26972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/03_2024/8csv_26972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/03_2024/8csv_26972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/03_2024/8csv_26972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/03_2024/8csv_26972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/03_2024/8csv_26972.pdb" } resolution = 2.7 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= 0.227 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 15 5.16 5 C 2286 2.51 5 N 677 2.21 5 O 734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "W TYR 21": "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: 3712 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3431 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 432} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 233 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Time building chain proxies: 2.38, per 1000 atoms: 0.64 Number of scatterers: 3712 At special positions: 0 Unit cell: (92.13, 110.39, 60.59, 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 15 16.00 O 734 8.00 N 677 7.00 C 2286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 773.5 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 65.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.541A pdb=" N GLU A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.545A pdb=" N ASN A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 449 through 460 removed outlier: 3.596A pdb=" N LYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 7 Processing helix chain 'W' and resid 8 through 17 Processing helix chain 'W' and resid 18 through 22 190 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1285 1.34 - 1.46: 646 1.46 - 1.58: 1770 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3726 Sorted by residual: bond pdb=" C LEU A 417 " pdb=" N PRO A 418 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.27e-01 bond pdb=" CA VAL A 437 " pdb=" CB VAL A 437 " ideal model delta sigma weight residual 1.540 1.550 -0.009 1.36e-02 5.41e+03 4.87e-01 bond pdb=" C ASP W 25 " pdb=" N ILE W 26 " ideal model delta sigma weight residual 1.330 1.325 0.005 8.40e-03 1.42e+04 3.42e-01 bond pdb=" CA LEU A 417 " pdb=" C LEU A 417 " ideal model delta sigma weight residual 1.520 1.527 -0.007 1.23e-02 6.61e+03 3.41e-01 bond pdb=" N PRO W 24 " pdb=" CA PRO W 24 " ideal model delta sigma weight residual 1.469 1.476 -0.007 1.28e-02 6.10e+03 3.40e-01 ... (remaining 3721 not shown) Histogram of bond angle deviations from ideal: 100.25 - 106.46: 117 106.46 - 112.68: 2031 112.68 - 118.89: 1024 118.89 - 125.11: 1840 125.11 - 131.32: 49 Bond angle restraints: 5061 Sorted by residual: angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 113.39 109.15 4.24 1.47e+00 4.63e-01 8.33e+00 angle pdb=" C LYS A 436 " pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 121.97 127.12 -5.15 1.80e+00 3.09e-01 8.17e+00 angle pdb=" CA VAL A 172 " pdb=" C VAL A 172 " pdb=" N ARG A 173 " ideal model delta sigma weight residual 118.55 116.70 1.85 8.60e-01 1.35e+00 4.60e+00 angle pdb=" O ASP A 337 " pdb=" C ASP A 337 " pdb=" N HIS A 338 " ideal model delta sigma weight residual 122.39 124.83 -2.44 1.29e+00 6.01e-01 3.58e+00 angle pdb=" CA VAL A 437 " pdb=" CB VAL A 437 " pdb=" CG1 VAL A 437 " ideal model delta sigma weight residual 110.40 113.35 -2.95 1.70e+00 3.46e-01 3.01e+00 ... (remaining 5056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 2127 17.25 - 34.50: 107 34.50 - 51.76: 25 51.76 - 69.01: 8 69.01 - 86.26: 2 Dihedral angle restraints: 2269 sinusoidal: 876 harmonic: 1393 Sorted by residual: dihedral pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " pdb=" CG ARG A 173 " pdb=" CD ARG A 173 " ideal model delta sinusoidal sigma weight residual -180.00 -121.72 -58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG A 187 " pdb=" CB ARG A 187 " pdb=" CG ARG A 187 " pdb=" CD ARG A 187 " ideal model delta sinusoidal sigma weight residual -180.00 -121.75 -58.25 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " pdb=" CD GLU A 96 " pdb=" OE1 GLU A 96 " ideal model delta sinusoidal sigma weight residual 0.00 83.13 -83.13 1 3.00e+01 1.11e-03 9.39e+00 ... (remaining 2266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 339 0.026 - 0.051: 157 0.051 - 0.077: 75 0.077 - 0.103: 22 0.103 - 0.128: 4 Chirality restraints: 597 Sorted by residual: chirality pdb=" CA ILE W 26 " pdb=" N ILE W 26 " pdb=" C ILE W 26 " pdb=" CB ILE W 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA LEU A 417 " pdb=" N LEU A 417 " pdb=" C LEU A 417 " pdb=" CB LEU A 417 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA PRO A 418 " pdb=" N PRO A 418 " pdb=" C PRO A 418 " pdb=" CB PRO A 418 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 594 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 439 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 440 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 307 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO A 308 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 373 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 374 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.021 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 716 2.78 - 3.31: 3724 3.31 - 3.84: 6586 3.84 - 4.37: 8167 4.37 - 4.90: 12809 Nonbonded interactions: 32002 Sorted by model distance: nonbonded pdb=" O PRO A 364 " pdb=" O HOH A1901 " model vdw 2.246 2.440 nonbonded pdb=" O ASP A 316 " pdb=" O HOH A1902 " model vdw 2.289 2.440 nonbonded pdb=" O LEU A 389 " pdb=" OG1 THR A 393 " model vdw 2.292 2.440 nonbonded pdb=" O VAL A 104 " pdb=" O HOH A1903 " model vdw 2.303 2.440 nonbonded pdb=" O HOH A1939 " pdb=" O HOH A1948 " model vdw 2.316 2.440 ... (remaining 31997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 6.070 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.100 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.002 0.021 3726 Z= 0.152 Angle : 0.467 5.577 5061 Z= 0.263 Chirality : 0.037 0.128 597 Planarity : 0.005 0.045 668 Dihedral : 11.849 86.262 1365 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 3.10 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.37), residues: 479 helix: 0.70 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 0.52 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 409 PHE 0.004 0.001 PHE A 234 TYR 0.010 0.001 TYR A 116 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.421 Fit side-chains REVERT: A 58 VAL cc_start: 0.8656 (t) cc_final: 0.8431 (m) REVERT: A 59 LYS cc_start: 0.7901 (mttm) cc_final: 0.7469 (mtpp) REVERT: A 91 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: A 96 GLU cc_start: 0.7738 (tp30) cc_final: 0.6904 (tp30) REVERT: A 157 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 182 ARG cc_start: 0.7744 (tmt-80) cc_final: 0.7502 (tmt-80) REVERT: A 289 GLU cc_start: 0.7960 (tt0) cc_final: 0.7756 (tt0) REVERT: A 303 LYS cc_start: 0.7742 (pttp) cc_final: 0.7247 (mttp) REVERT: A 337 ASP cc_start: 0.7711 (m-30) cc_final: 0.7314 (m-30) REVERT: A 402 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 421 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7778 (tttm) outliers start: 4 outliers final: 1 residues processed: 85 average time/residue: 1.1344 time to fit residues: 99.4939 Evaluate side-chains 63 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 370 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 165 ASN A 215 HIS A 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3726 Z= 0.175 Angle : 0.460 6.045 5061 Z= 0.240 Chirality : 0.037 0.135 597 Planarity : 0.005 0.038 668 Dihedral : 4.323 25.609 513 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.51 % Favored : 97.29 % Rotamer: Outliers : 2.33 % Allowed : 9.04 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.38), residues: 479 helix: 1.25 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.75 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 409 PHE 0.006 0.001 PHE A 234 TYR 0.010 0.001 TYR A 116 ARG 0.005 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.435 Fit side-chains REVERT: A 58 VAL cc_start: 0.8565 (t) cc_final: 0.8358 (m) REVERT: A 59 LYS cc_start: 0.7858 (mttm) cc_final: 0.7472 (mtpp) REVERT: A 68 GLU cc_start: 0.8160 (mp0) cc_final: 0.7727 (mt-10) REVERT: A 91 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 96 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6232 (tp30) REVERT: A 182 ARG cc_start: 0.7731 (tmt-80) cc_final: 0.7392 (tmt-80) REVERT: A 270 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7585 (pttm) REVERT: A 303 LYS cc_start: 0.7751 (pttp) cc_final: 0.7179 (mttp) REVERT: A 337 ASP cc_start: 0.7750 (m-30) cc_final: 0.7350 (m-30) REVERT: A 421 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7693 (tttm) outliers start: 9 outliers final: 3 residues processed: 68 average time/residue: 1.1012 time to fit residues: 77.5191 Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN A 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3726 Z= 0.146 Angle : 0.436 7.925 5061 Z= 0.222 Chirality : 0.036 0.125 597 Planarity : 0.004 0.036 668 Dihedral : 3.983 24.476 511 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.51 % Favored : 97.29 % Rotamer: Outliers : 2.07 % Allowed : 10.34 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.39), residues: 479 helix: 1.57 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.86 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 409 PHE 0.005 0.001 PHE A 234 TYR 0.008 0.001 TYR A 116 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.418 Fit side-chains REVERT: A 59 LYS cc_start: 0.7858 (mttm) cc_final: 0.7461 (mtpp) REVERT: A 68 GLU cc_start: 0.8143 (mp0) cc_final: 0.7691 (mt-10) REVERT: A 91 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: A 182 ARG cc_start: 0.7754 (tmt-80) cc_final: 0.7434 (tmt-80) REVERT: A 270 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7550 (pttm) REVERT: A 303 LYS cc_start: 0.7700 (pttp) cc_final: 0.7165 (mttp) REVERT: A 314 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: A 337 ASP cc_start: 0.7745 (m-30) cc_final: 0.7349 (m-30) REVERT: A 402 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: A 421 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7903 (tttm) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.1951 time to fit residues: 80.2722 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3726 Z= 0.171 Angle : 0.450 7.438 5061 Z= 0.229 Chirality : 0.037 0.126 597 Planarity : 0.004 0.036 668 Dihedral : 4.029 25.158 511 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 10.85 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.38), residues: 479 helix: 1.63 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.83 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.001 TYR A 116 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.469 Fit side-chains REVERT: A 59 LYS cc_start: 0.7873 (mttm) cc_final: 0.7475 (mtpp) REVERT: A 68 GLU cc_start: 0.8153 (mp0) cc_final: 0.7690 (mt-10) REVERT: A 91 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: A 96 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: A 182 ARG cc_start: 0.7778 (tmt-80) cc_final: 0.7459 (tmt-80) REVERT: A 270 LYS cc_start: 0.7854 (ptpt) cc_final: 0.7530 (pttm) REVERT: A 303 LYS cc_start: 0.7690 (pttp) cc_final: 0.7185 (mttp) REVERT: A 314 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: A 337 ASP cc_start: 0.7740 (m-30) cc_final: 0.7339 (m-30) REVERT: A 402 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: A 421 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7853 (tttm) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 1.1401 time to fit residues: 79.0065 Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.129 Angle : 0.432 7.943 5061 Z= 0.218 Chirality : 0.035 0.126 597 Planarity : 0.004 0.035 668 Dihedral : 3.858 24.556 511 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 2.33 % Allowed : 11.37 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.39), residues: 479 helix: 1.82 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.91 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 409 PHE 0.005 0.001 PHE A 413 TYR 0.007 0.001 TYR A 116 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.424 Fit side-chains REVERT: A 59 LYS cc_start: 0.7883 (mttm) cc_final: 0.7477 (mtpp) REVERT: A 68 GLU cc_start: 0.8135 (mp0) cc_final: 0.7665 (mt-10) REVERT: A 91 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: A 96 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: A 182 ARG cc_start: 0.7768 (tmt-80) cc_final: 0.7455 (tmt-80) REVERT: A 270 LYS cc_start: 0.7793 (ptpt) cc_final: 0.7520 (pttm) REVERT: A 303 LYS cc_start: 0.7657 (pttp) cc_final: 0.7164 (mttp) REVERT: A 314 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: A 337 ASP cc_start: 0.7741 (m-30) cc_final: 0.7346 (m-30) REVERT: A 402 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: A 421 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7867 (tttm) outliers start: 9 outliers final: 3 residues processed: 65 average time/residue: 1.1547 time to fit residues: 77.6817 Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3726 Z= 0.113 Angle : 0.414 7.491 5061 Z= 0.208 Chirality : 0.035 0.129 597 Planarity : 0.004 0.033 668 Dihedral : 3.700 24.231 511 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 11.89 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.39), residues: 479 helix: 1.96 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.97 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 162 PHE 0.004 0.001 PHE A 413 TYR 0.005 0.001 TYR A 116 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.461 Fit side-chains REVERT: A 59 LYS cc_start: 0.7892 (mttm) cc_final: 0.7460 (mtpp) REVERT: A 68 GLU cc_start: 0.8091 (mp0) cc_final: 0.7636 (mt-10) REVERT: A 91 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: A 182 ARG cc_start: 0.7760 (tmt-80) cc_final: 0.7462 (tmt-80) REVERT: A 270 LYS cc_start: 0.7761 (ptpt) cc_final: 0.7448 (pttm) REVERT: A 303 LYS cc_start: 0.7623 (pttp) cc_final: 0.7137 (mttp) REVERT: A 314 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: A 337 ASP cc_start: 0.7730 (m-30) cc_final: 0.7346 (m-30) REVERT: A 402 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 421 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7906 (tttm) REVERT: A 451 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6678 (tp30) outliers start: 11 outliers final: 3 residues processed: 65 average time/residue: 1.1549 time to fit residues: 77.7436 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3726 Z= 0.241 Angle : 0.499 9.369 5061 Z= 0.252 Chirality : 0.039 0.126 597 Planarity : 0.004 0.033 668 Dihedral : 4.166 25.276 511 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 3.36 % Allowed : 12.40 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.38), residues: 479 helix: 1.68 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.75 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 409 PHE 0.007 0.001 PHE A 234 TYR 0.012 0.002 TYR A 116 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.461 Fit side-chains REVERT: A 59 LYS cc_start: 0.7872 (mttm) cc_final: 0.7453 (mtpp) REVERT: A 68 GLU cc_start: 0.8163 (mp0) cc_final: 0.7671 (mt-10) REVERT: A 91 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: A 96 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6500 (tp30) REVERT: A 182 ARG cc_start: 0.7828 (tmt-80) cc_final: 0.7489 (tmt-80) REVERT: A 270 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7489 (pttm) REVERT: A 303 LYS cc_start: 0.7716 (pttp) cc_final: 0.7203 (mttp) REVERT: A 314 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 337 ASP cc_start: 0.7741 (m-30) cc_final: 0.7336 (m-30) REVERT: A 402 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: A 421 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7865 (tttm) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 1.1239 time to fit residues: 76.8865 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 18 optimal weight: 20.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3726 Z= 0.132 Angle : 0.445 9.676 5061 Z= 0.222 Chirality : 0.036 0.129 597 Planarity : 0.004 0.032 668 Dihedral : 3.867 24.392 511 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 13.44 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.39), residues: 479 helix: 1.87 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.95 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 409 PHE 0.005 0.001 PHE A 413 TYR 0.007 0.001 TYR A 116 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.424 Fit side-chains REVERT: A 59 LYS cc_start: 0.7885 (mttm) cc_final: 0.7440 (mtpp) REVERT: A 68 GLU cc_start: 0.8123 (mp0) cc_final: 0.7672 (mt-10) REVERT: A 91 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: A 96 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: A 182 ARG cc_start: 0.7801 (tmt-80) cc_final: 0.7483 (tmt-80) REVERT: A 270 LYS cc_start: 0.7762 (ptpt) cc_final: 0.7446 (pttm) REVERT: A 303 LYS cc_start: 0.7639 (pttp) cc_final: 0.7158 (mttp) REVERT: A 314 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: A 337 ASP cc_start: 0.7733 (m-30) cc_final: 0.7349 (m-30) REVERT: A 402 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: A 421 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7930 (tttm) REVERT: A 451 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6673 (tp30) outliers start: 10 outliers final: 3 residues processed: 63 average time/residue: 1.1131 time to fit residues: 72.6807 Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 0.0030 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3726 Z= 0.114 Angle : 0.435 10.340 5061 Z= 0.213 Chirality : 0.035 0.127 597 Planarity : 0.004 0.031 668 Dihedral : 3.621 23.552 511 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 1.81 % Allowed : 14.47 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.39), residues: 479 helix: 2.03 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.01 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 409 PHE 0.004 0.001 PHE A 413 TYR 0.004 0.001 TYR A 116 ARG 0.007 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.431 Fit side-chains REVERT: A 59 LYS cc_start: 0.7877 (mttm) cc_final: 0.7456 (mtpp) REVERT: A 68 GLU cc_start: 0.8070 (mp0) cc_final: 0.7638 (mt-10) REVERT: A 91 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: A 182 ARG cc_start: 0.7792 (tmt-80) cc_final: 0.7496 (tmt-80) REVERT: A 270 LYS cc_start: 0.7722 (ptpt) cc_final: 0.7415 (pttm) REVERT: A 303 LYS cc_start: 0.7610 (pttp) cc_final: 0.7111 (mttp) REVERT: A 314 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: A 402 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: A 403 SER cc_start: 0.8233 (m) cc_final: 0.7947 (p) REVERT: A 421 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7913 (tttm) REVERT: A 451 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6652 (tp30) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 1.1582 time to fit residues: 79.0704 Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.0010 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3726 Z= 0.129 Angle : 0.454 10.596 5061 Z= 0.222 Chirality : 0.035 0.127 597 Planarity : 0.004 0.031 668 Dihedral : 3.664 23.870 511 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.34 % Favored : 96.45 % Rotamer: Outliers : 2.33 % Allowed : 14.47 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.39), residues: 479 helix: 2.01 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.05 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 409 PHE 0.004 0.001 PHE A 234 TYR 0.006 0.001 TYR A 116 ARG 0.007 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.420 Fit side-chains REVERT: A 59 LYS cc_start: 0.7879 (mttm) cc_final: 0.7429 (mtpp) REVERT: A 68 GLU cc_start: 0.8070 (mp0) cc_final: 0.7603 (mt-10) REVERT: A 91 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: A 182 ARG cc_start: 0.7798 (tmt-80) cc_final: 0.7498 (tmt-80) REVERT: A 270 LYS cc_start: 0.7716 (ptpt) cc_final: 0.7404 (pttm) REVERT: A 303 LYS cc_start: 0.7613 (pttp) cc_final: 0.7121 (mttp) REVERT: A 402 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: A 403 SER cc_start: 0.8249 (m) cc_final: 0.7954 (p) REVERT: A 421 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7872 (tttm) REVERT: A 451 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6639 (tp30) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 1.1405 time to fit residues: 73.2410 Evaluate side-chains 65 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.114622 restraints weight = 3894.553| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.35 r_work: 0.3043 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3726 Z= 0.170 Angle : 0.478 10.653 5061 Z= 0.237 Chirality : 0.037 0.128 597 Planarity : 0.004 0.031 668 Dihedral : 3.885 24.491 511 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 14.21 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.39), residues: 479 helix: 1.89 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.92 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 409 PHE 0.006 0.001 PHE A 234 TYR 0.008 0.001 TYR A 116 ARG 0.006 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.24 seconds wall clock time: 37 minutes 57.85 seconds (2277.85 seconds total)