Starting phenix.real_space_refine on Wed Mar 5 21:10:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csv_26972/03_2025/8csv_26972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csv_26972/03_2025/8csv_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/cci-nas-00/data/ceres_data/8csv_26972/03_2025/8csv_26972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csv_26972/03_2025/8csv_26972.map" model { file = "/net/cci-nas-00/data/ceres_data/8csv_26972/03_2025/8csv_26972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csv_26972/03_2025/8csv_26972.cif" } 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. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.17, per 1000 atoms: 0.85 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 - 3.00 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 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 462.7 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: 0.41 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: 0.89 Time building geometry restraints manager: 1.11 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: 0.00 - 1.12: 4917 1.12 - 2.23: 114 2.23 - 3.35: 19 3.35 - 4.46: 9 4.46 - 5.58: 2 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 3.040 nonbonded pdb=" O ASP A 316 " pdb=" O HOH A1902 " model vdw 2.289 3.040 nonbonded pdb=" O LEU A 389 " pdb=" OG1 THR A 393 " model vdw 2.292 3.040 nonbonded pdb=" O VAL A 104 " pdb=" O HOH A1903 " model vdw 2.303 3.040 nonbonded pdb=" O HOH A1939 " pdb=" O HOH A1948 " model vdw 2.316 3.040 ... (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 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 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: 2.280 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.388 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: 1.1550 time to fit residues: 101.2718 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.140264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117556 restraints weight = 3876.836| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.27 r_work: 0.3071 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1333 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= 0.137 Angle : 0.446 6.308 5061 Z= 0.231 Chirality : 0.036 0.124 597 Planarity : 0.005 0.037 668 Dihedral : 4.109 23.742 513 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 9.04 % Favored : 89.41 % 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: 1.63 (0.38), residues: 479 helix: 1.30 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.89 (0.54), 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 0.008 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 69 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.441 Fit side-chains REVERT: A 59 LYS cc_start: 0.8065 (mttm) cc_final: 0.7740 (mtpp) REVERT: A 68 GLU cc_start: 0.8376 (mp0) cc_final: 0.7950 (mt-10) REVERT: A 91 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: A 96 GLU cc_start: 0.7852 (tp30) cc_final: 0.6630 (tp30) REVERT: A 182 ARG cc_start: 0.7995 (tmt-80) cc_final: 0.7591 (tmt-80) REVERT: A 270 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7712 (pttm) REVERT: A 303 LYS cc_start: 0.7876 (pttp) cc_final: 0.7232 (mttp) REVERT: A 337 ASP cc_start: 0.8000 (m-30) cc_final: 0.7670 (m-30) REVERT: A 421 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8077 (tttm) REVERT: A 446 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7569 (ttm-80) REVERT: A 451 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: W 11 MET cc_start: 0.6108 (tpp) cc_final: 0.5780 (tpp) outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 1.2984 time to fit residues: 85.7928 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 451 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 215 HIS A 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.141023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.118379 restraints weight = 3841.246| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.27 r_work: 0.3101 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3726 Z= 0.117 Angle : 0.406 5.040 5061 Z= 0.211 Chirality : 0.035 0.127 597 Planarity : 0.004 0.034 668 Dihedral : 3.775 22.848 511 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.30 % Favored : 97.49 % Rotamer: Outliers : 1.81 % Allowed : 10.85 % Favored : 87.34 % 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: 2.07 (0.39), residues: 479 helix: 1.66 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.02 (0.55), 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 0.006 0.001 TYR A 116 ARG 0.003 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 70 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.427 Fit side-chains REVERT: A 59 LYS cc_start: 0.8059 (mttm) cc_final: 0.7716 (mtpp) REVERT: A 68 GLU cc_start: 0.8345 (mp0) cc_final: 0.7937 (mt-10) REVERT: A 91 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: A 96 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6801 (tp30) REVERT: A 182 ARG cc_start: 0.7975 (tmt-80) cc_final: 0.7554 (tmt-80) REVERT: A 270 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7704 (pttm) REVERT: A 303 LYS cc_start: 0.7866 (pttp) cc_final: 0.7246 (mttp) REVERT: A 337 ASP cc_start: 0.7974 (m-30) cc_final: 0.7612 (m-30) REVERT: A 402 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 421 LYS cc_start: 0.8444 (ttmm) cc_final: 0.7960 (tttm) REVERT: W 11 MET cc_start: 0.5960 (tpp) cc_final: 0.5578 (tpp) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 1.1960 time to fit residues: 81.7031 Evaluate side-chains 67 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115675 restraints weight = 3874.490| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.28 r_work: 0.3049 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1542 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 : 0.435 5.064 5061 Z= 0.226 Chirality : 0.037 0.127 597 Planarity : 0.004 0.036 668 Dihedral : 3.939 23.344 511 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer: Outliers : 2.07 % Allowed : 11.89 % Favored : 86.05 % 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: 2.09 (0.39), residues: 479 helix: 1.69 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.96 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.007 0.001 PHE A 234 TYR 0.010 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 71 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.474 Fit side-chains REVERT: A 59 LYS cc_start: 0.8057 (mttm) cc_final: 0.7716 (mtpp) REVERT: A 68 GLU cc_start: 0.8404 (mp0) cc_final: 0.7974 (mt-10) REVERT: A 91 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: A 96 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: A 182 ARG cc_start: 0.7979 (tmt-80) cc_final: 0.7550 (tmt-80) REVERT: A 270 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7695 (pttm) REVERT: A 303 LYS cc_start: 0.7862 (pttp) cc_final: 0.7249 (mttp) REVERT: A 337 ASP cc_start: 0.7986 (m-30) cc_final: 0.7635 (m-30) REVERT: A 402 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 421 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8135 (tttm) REVERT: W 11 MET cc_start: 0.5903 (tpp) cc_final: 0.5504 (tpp) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 1.2760 time to fit residues: 86.9726 Evaluate side-chains 68 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 45 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.139769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.116889 restraints weight = 3905.437| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.29 r_work: 0.3068 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3726 Z= 0.139 Angle : 0.418 5.038 5061 Z= 0.216 Chirality : 0.036 0.127 597 Planarity : 0.004 0.035 668 Dihedral : 3.822 22.950 511 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer: Outliers : 2.07 % Allowed : 12.40 % Favored : 85.53 % 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: 2.27 (0.39), residues: 479 helix: 1.82 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 1.06 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.005 0.001 PHE A 413 TYR 0.007 0.001 TYR A 116 ARG 0.003 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 67 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.444 Fit side-chains REVERT: A 59 LYS cc_start: 0.8049 (mttm) cc_final: 0.7711 (mtpp) REVERT: A 68 GLU cc_start: 0.8387 (mp0) cc_final: 0.7964 (mt-10) REVERT: A 91 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 96 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: A 182 ARG cc_start: 0.7983 (tmt-80) cc_final: 0.7546 (tmt-80) REVERT: A 270 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7708 (pttm) REVERT: A 272 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 303 LYS cc_start: 0.7800 (pttp) cc_final: 0.7216 (mttp) REVERT: A 337 ASP cc_start: 0.7988 (m-30) cc_final: 0.7677 (m-30) REVERT: A 402 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 421 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8157 (tttm) REVERT: W 11 MET cc_start: 0.5867 (tpp) cc_final: 0.5457 (tpp) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 1.2100 time to fit residues: 75.1337 Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.138790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115606 restraints weight = 3913.868| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.30 r_work: 0.3053 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3726 Z= 0.161 Angle : 0.433 5.040 5061 Z= 0.223 Chirality : 0.037 0.127 597 Planarity : 0.004 0.036 668 Dihedral : 3.884 23.201 511 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 2.07 % Allowed : 13.44 % Favored : 84.50 % 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: 2.26 (0.39), residues: 479 helix: 1.83 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.02 (0.55), 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 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 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.400 Fit side-chains REVERT: A 59 LYS cc_start: 0.8077 (mttm) cc_final: 0.7731 (mtpp) REVERT: A 68 GLU cc_start: 0.8383 (mp0) cc_final: 0.7974 (mt-10) REVERT: A 91 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: A 96 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: A 182 ARG cc_start: 0.7987 (tmt-80) cc_final: 0.7536 (tmt-80) REVERT: A 270 LYS cc_start: 0.7979 (ptpt) cc_final: 0.7677 (pttm) REVERT: A 272 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 303 LYS cc_start: 0.7813 (pttp) cc_final: 0.7236 (mttp) REVERT: A 337 ASP cc_start: 0.8016 (m-30) cc_final: 0.7716 (m-30) REVERT: A 402 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: A 421 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8121 (tttm) REVERT: W 11 MET cc_start: 0.5869 (tpp) cc_final: 0.5561 (tpp) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 1.1290 time to fit residues: 70.2253 Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 LEU 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 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.139215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.116188 restraints weight = 3896.958| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.29 r_work: 0.3073 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3726 Z= 0.149 Angle : 0.431 5.528 5061 Z= 0.221 Chirality : 0.036 0.128 597 Planarity : 0.004 0.036 668 Dihedral : 3.867 23.110 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 2.58 % Allowed : 12.66 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.39), residues: 479 helix: 1.84 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.05 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.005 0.001 PHE A 234 TYR 0.008 0.001 TYR A 116 ARG 0.003 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 70 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.417 Fit side-chains REVERT: A 59 LYS cc_start: 0.8072 (mttm) cc_final: 0.7731 (mtpp) REVERT: A 68 GLU cc_start: 0.8382 (mp0) cc_final: 0.7941 (mt-10) REVERT: A 91 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 96 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: A 182 ARG cc_start: 0.7989 (tmt-80) cc_final: 0.7535 (tmt-80) REVERT: A 270 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7666 (pttm) REVERT: A 272 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 303 LYS cc_start: 0.7813 (pttp) cc_final: 0.7240 (mttp) REVERT: A 314 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 337 ASP cc_start: 0.8021 (m-30) cc_final: 0.7716 (m-30) REVERT: A 402 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: A 421 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8154 (tttm) REVERT: W 11 MET cc_start: 0.5858 (tpp) cc_final: 0.5552 (tpp) outliers start: 10 outliers final: 3 residues processed: 63 average time/residue: 1.1468 time to fit residues: 74.7807 Evaluate side-chains 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 LEU Chi-restraints excluded: chain A residue 402 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.136517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113282 restraints weight = 3941.728| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.30 r_work: 0.3026 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3726 Z= 0.229 Angle : 0.481 5.927 5061 Z= 0.248 Chirality : 0.039 0.128 597 Planarity : 0.004 0.036 668 Dihedral : 4.147 24.090 511 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.55 % Favored : 96.24 % Rotamer: Outliers : 2.33 % Allowed : 13.18 % Favored : 84.50 % 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: 2.01 (0.39), residues: 479 helix: 1.64 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.91 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 383 PHE 0.008 0.001 PHE A 234 TYR 0.011 0.002 TYR A 116 ARG 0.003 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 69 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.377 Fit side-chains REVERT: A 59 LYS cc_start: 0.8076 (mttm) cc_final: 0.7732 (mtpp) REVERT: A 68 GLU cc_start: 0.8436 (mp0) cc_final: 0.7973 (mt-10) REVERT: A 91 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: A 96 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: A 182 ARG cc_start: 0.8001 (tmt-80) cc_final: 0.7543 (tmt-80) REVERT: A 270 LYS cc_start: 0.7986 (ptpt) cc_final: 0.7680 (pttm) REVERT: A 303 LYS cc_start: 0.7849 (pttp) cc_final: 0.7271 (mttp) REVERT: A 337 ASP cc_start: 0.8019 (m-30) cc_final: 0.7680 (m-30) REVERT: A 402 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 421 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8152 (tttm) REVERT: A 451 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: W 11 MET cc_start: 0.5920 (tpp) cc_final: 0.5604 (tpp) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 1.1053 time to fit residues: 71.0155 Evaluate side-chains 68 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.116776 restraints weight = 3863.801| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.29 r_work: 0.3066 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3726 Z= 0.133 Angle : 0.427 5.994 5061 Z= 0.219 Chirality : 0.036 0.128 597 Planarity : 0.004 0.036 668 Dihedral : 3.816 22.968 511 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 1.55 % Allowed : 14.21 % 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: 2.36 (0.39), residues: 479 helix: 1.89 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 1.10 (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 0.006 0.001 TYR A 116 ARG 0.004 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 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.446 Fit side-chains REVERT: A 59 LYS cc_start: 0.8071 (mttm) cc_final: 0.7700 (mtpp) REVERT: A 68 GLU cc_start: 0.8387 (mp0) cc_final: 0.7938 (mt-10) REVERT: A 91 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: A 182 ARG cc_start: 0.7979 (tmt-80) cc_final: 0.7528 (tmt-80) REVERT: A 270 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7630 (pttm) REVERT: A 272 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 303 LYS cc_start: 0.7794 (pttp) cc_final: 0.7215 (mttp) REVERT: A 337 ASP cc_start: 0.7994 (m-30) cc_final: 0.7690 (m-30) REVERT: A 402 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 421 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8142 (tttm) REVERT: A 451 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: W 11 MET cc_start: 0.5861 (tpp) cc_final: 0.5565 (tpp) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 1.1555 time to fit residues: 71.9453 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 389 LEU 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 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 165 ASN A 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.139601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116748 restraints weight = 3882.605| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.28 r_work: 0.3066 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 : 0.002 0.027 3726 Z= 0.138 Angle : 0.432 6.025 5061 Z= 0.221 Chirality : 0.036 0.128 597 Planarity : 0.004 0.035 668 Dihedral : 3.782 22.730 511 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 1.55 % Allowed : 14.21 % 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: 2.37 (0.39), residues: 479 helix: 1.91 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.05 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 409 PHE 0.004 0.001 PHE A 234 TYR 0.006 0.001 TYR A 116 ARG 0.004 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 60 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.399 Fit side-chains REVERT: A 59 LYS cc_start: 0.8078 (mttm) cc_final: 0.7706 (mtpp) REVERT: A 68 GLU cc_start: 0.8386 (mp0) cc_final: 0.7939 (mt-10) REVERT: A 91 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: A 96 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: A 182 ARG cc_start: 0.7987 (tmt-80) cc_final: 0.7537 (tmt-80) REVERT: A 270 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7624 (pttm) REVERT: A 272 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 303 LYS cc_start: 0.7789 (pttp) cc_final: 0.7205 (mttp) REVERT: A 337 ASP cc_start: 0.7998 (m-30) cc_final: 0.7658 (m-30) REVERT: A 402 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 421 LYS cc_start: 0.8444 (ttmm) cc_final: 0.8154 (tttm) REVERT: W 11 MET cc_start: 0.5873 (tpp) cc_final: 0.5579 (tpp) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 1.2582 time to fit residues: 71.7491 Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.138496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115405 restraints weight = 3917.471| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.29 r_work: 0.3046 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3726 Z= 0.165 Angle : 0.448 6.068 5061 Z= 0.229 Chirality : 0.037 0.127 597 Planarity : 0.004 0.035 668 Dihedral : 3.887 23.032 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.34 % Favored : 96.45 % Rotamer: Outliers : 2.33 % Allowed : 13.18 % Favored : 84.50 % 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: 2.27 (0.39), residues: 479 helix: 1.83 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 1.04 (0.55), 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 0.008 0.001 TYR A 116 ARG 0.004 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.08 seconds wall clock time: 63 minutes 1.90 seconds (3781.90 seconds total)