Starting phenix.real_space_refine on Wed Jul 1 21:39:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kq5_62496/07_2026/9kq5_62496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kq5_62496/07_2026/9kq5_62496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kq5_62496/07_2026/9kq5_62496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kq5_62496/07_2026/9kq5_62496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kq5_62496/07_2026/9kq5_62496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kq5_62496/07_2026/9kq5_62496.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.077 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 17 5.16 5 C 1966 2.51 5 N 478 2.21 5 O 509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2970 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2970 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 27, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'ASP:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 1.03, per 1000 atoms: 0.35 Number of scatterers: 2970 At special positions: 0 Unit cell: (54.056, 72.696, 77.356, 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 17 16.00 O 509 8.00 N 478 7.00 C 1966 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: 0.31 Conformation dependent library (CDL) restraints added in 146.2 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 26 through 53 removed outlier: 4.170A pdb=" N ILE A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 121 through 148 removed outlier: 4.587A pdb=" N LYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 140 - end of helix Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 151 through 171 removed outlier: 3.693A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 204 removed outlier: 4.912A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.581A pdb=" N ARG A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 4.142A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.536A pdb=" N ASP A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 Proline residue: A 304 - end of helix removed outlier: 3.726A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.501A pdb=" N HIS A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 Processing helix chain 'A' and resid 379 through 413 Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 417 through 446 removed outlier: 3.625A pdb=" N ALA A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 5.893A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 471 through 475 252 hydrogen bonds defined for protein. 741 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: 0.48 Time building geometry restraints manager: 0.41 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: 921 1.34 - 1.46: 603 1.46 - 1.58: 1492 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3044 Sorted by residual: bond pdb=" CA ASN A 275 " pdb=" C ASN A 275 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.12e-02 7.97e+03 2.42e+00 bond pdb=" C GLU A 309 " pdb=" N PRO A 310 " ideal model delta sigma weight residual 1.331 1.341 -0.009 7.90e-03 1.60e+04 1.37e+00 bond pdb=" C PRO A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.18e+00 bond pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 1.524 1.535 -0.010 1.05e-02 9.07e+03 9.27e-01 bond pdb=" C LEU A 405 " pdb=" N ALA A 406 " ideal model delta sigma weight residual 1.334 1.322 0.012 1.27e-02 6.20e+03 9.14e-01 ... (remaining 3039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 4039 1.59 - 3.19: 98 3.19 - 4.78: 26 4.78 - 6.38: 10 6.38 - 7.97: 1 Bond angle restraints: 4174 Sorted by residual: angle pdb=" C VAL A 374 " pdb=" N PRO A 375 " pdb=" CA PRO A 375 " ideal model delta sigma weight residual 119.05 114.98 4.07 1.11e+00 8.12e-01 1.35e+01 angle pdb=" N SER A 419 " pdb=" CA SER A 419 " pdb=" C SER A 419 " ideal model delta sigma weight residual 111.14 114.49 -3.35 1.08e+00 8.57e-01 9.62e+00 angle pdb=" N HIS A 413 " pdb=" CA HIS A 413 " pdb=" C HIS A 413 " ideal model delta sigma weight residual 108.45 112.34 -3.89 1.26e+00 6.30e-01 9.52e+00 angle pdb=" N ILE A 437 " pdb=" CA ILE A 437 " pdb=" C ILE A 437 " ideal model delta sigma weight residual 111.48 108.84 2.64 9.40e-01 1.13e+00 7.89e+00 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 110.70 113.92 -3.22 1.22e+00 6.72e-01 6.98e+00 ... (remaining 4169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 1604 16.36 - 32.72: 149 32.72 - 49.09: 27 49.09 - 65.45: 8 65.45 - 81.81: 2 Dihedral angle restraints: 1790 sinusoidal: 620 harmonic: 1170 Sorted by residual: dihedral pdb=" CA GLN A 26 " pdb=" CB GLN A 26 " pdb=" CG GLN A 26 " pdb=" CD GLN A 26 " ideal model delta sinusoidal sigma weight residual 180.00 -122.94 -57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA LEU A 141 " pdb=" CB LEU A 141 " pdb=" CG LEU A 141 " pdb=" CD1 LEU A 141 " ideal model delta sinusoidal sigma weight residual 180.00 125.00 55.00 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" CB GLU A 309 " pdb=" CG GLU A 309 " ideal model delta sinusoidal sigma weight residual -180.00 -126.34 -53.66 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 1787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 278 0.022 - 0.045: 105 0.045 - 0.067: 71 0.067 - 0.089: 33 0.089 - 0.111: 25 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" C PRO A 304 " pdb=" CB PRO A 304 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA THR A 345 " pdb=" N THR A 345 " pdb=" C THR A 345 " pdb=" CB THR A 345 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 3.05e-01 chirality pdb=" CA LEU A 401 " pdb=" N LEU A 401 " pdb=" C LEU A 401 " pdb=" CB LEU A 401 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 509 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 204 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 205 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 27 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 28 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 112 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 113 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.017 5.00e-02 4.00e+02 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 800 2.80 - 3.32: 3165 3.32 - 3.85: 5226 3.85 - 4.37: 5792 4.37 - 4.90: 9800 Nonbonded interactions: 24783 Sorted by model distance: nonbonded pdb=" O GLY A 186 " pdb=" OG SER A 189 " model vdw 2.273 3.040 nonbonded pdb=" O LEU A 127 " pdb=" OG SER A 130 " model vdw 2.374 3.040 nonbonded pdb=" O MET A 162 " pdb=" OG1 THR A 166 " model vdw 2.410 3.040 nonbonded pdb=" O ASP A 425 " pdb=" OG SER A 429 " model vdw 2.422 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 119 " model vdw 2.458 3.040 ... (remaining 24778 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: 0.010 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.470 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.004 0.033 3044 Z= 0.190 Angle : 0.675 7.969 4174 Z= 0.379 Chirality : 0.040 0.111 512 Planarity : 0.005 0.045 520 Dihedral : 13.658 81.811 1038 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.00 % Allowed : 13.33 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.40), residues: 400 helix: -0.28 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -3.15 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 30 TYR 0.017 0.001 TYR A 428 PHE 0.008 0.001 PHE A 392 TRP 0.004 0.001 TRP A 331 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 3044) covalent geometry : angle 0.67510 / 0.38 ( 4174) hydrogen bonds : bond 0.13745 / 8.81 ( 252) hydrogen bonds : angle 5.88678 / 4.23 ( 741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.063 Fit side-chains REVERT: A 222 SER cc_start: 0.7830 (t) cc_final: 0.7508 (p) REVERT: A 235 LEU cc_start: 0.6951 (tp) cc_final: 0.6648 (mp) REVERT: A 236 TYR cc_start: 0.8104 (t80) cc_final: 0.6857 (t80) REVERT: A 286 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.6892 (mtt) REVERT: A 288 ASP cc_start: 0.7428 (t70) cc_final: 0.7070 (t70) REVERT: A 300 THR cc_start: 0.8386 (m) cc_final: 0.8077 (p) REVERT: A 305 LEU cc_start: 0.8292 (tp) cc_final: 0.8018 (tp) REVERT: A 419 SER cc_start: 0.7527 (t) cc_final: 0.6966 (m) outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.0332 time to fit residues: 3.1794 Evaluate side-chains 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.196068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164482 restraints weight = 3376.412| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.88 r_work: 0.3815 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3044 Z= 0.146 Angle : 0.650 6.823 4174 Z= 0.310 Chirality : 0.040 0.114 512 Planarity : 0.006 0.035 520 Dihedral : 4.464 33.975 437 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.00 % Allowed : 15.67 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.43), residues: 400 helix: 1.11 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -2.02 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.011 0.002 TYR A 428 PHE 0.010 0.001 PHE A 392 TRP 0.004 0.001 TRP A 315 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 3044) covalent geometry : angle 0.65023 / 0.31 ( 4174) hydrogen bonds : bond 0.04064 / 2.68 ( 252) hydrogen bonds : angle 4.16549 / 3.03 ( 741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.106 Fit side-chains REVERT: A 26 GLN cc_start: 0.5614 (OUTLIER) cc_final: 0.4177 (tp40) REVERT: A 235 LEU cc_start: 0.7941 (tp) cc_final: 0.7607 (mp) REVERT: A 242 ARG cc_start: 0.6958 (mmm-85) cc_final: 0.6754 (mmm-85) REVERT: A 286 MET cc_start: 0.7744 (tpt) cc_final: 0.7112 (mtt) REVERT: A 457 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5970 (tp) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 0.0533 time to fit residues: 4.2216 Evaluate side-chains 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.197383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165784 restraints weight = 3368.858| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.88 r_work: 0.3824 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3044 Z= 0.130 Angle : 0.630 7.424 4174 Z= 0.295 Chirality : 0.039 0.111 512 Planarity : 0.005 0.031 520 Dihedral : 3.815 13.862 433 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.33 % Allowed : 17.67 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.44), residues: 400 helix: 1.52 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.60 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.010 0.001 TYR A 290 PHE 0.014 0.001 PHE A 407 TRP 0.005 0.001 TRP A 315 HIS 0.006 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3044) covalent geometry : angle 0.63006 / 0.30 ( 4174) hydrogen bonds : bond 0.03638 / 2.40 ( 252) hydrogen bonds : angle 3.99927 / 2.92 ( 741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.105 Fit side-chains REVERT: A 26 GLN cc_start: 0.5452 (OUTLIER) cc_final: 0.4144 (tp40) REVERT: A 152 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6988 (p0) REVERT: A 235 LEU cc_start: 0.7924 (tp) cc_final: 0.7561 (mp) REVERT: A 286 MET cc_start: 0.7750 (tpt) cc_final: 0.7045 (mtt) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 0.0566 time to fit residues: 4.0893 Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.196125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164337 restraints weight = 3371.883| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.86 r_work: 0.3773 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3044 Z= 0.133 Angle : 0.624 7.195 4174 Z= 0.293 Chirality : 0.040 0.113 512 Planarity : 0.005 0.032 520 Dihedral : 3.745 13.176 433 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.33 % Allowed : 16.33 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.44), residues: 400 helix: 1.75 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.39 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.010 0.001 TYR A 421 PHE 0.011 0.001 PHE A 392 TRP 0.005 0.001 TRP A 315 HIS 0.004 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 3044) covalent geometry : angle 0.62427 / 0.29 ( 4174) hydrogen bonds : bond 0.03554 / 2.36 ( 252) hydrogen bonds : angle 3.92477 / 2.87 ( 741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.105 Fit side-chains REVERT: A 26 GLN cc_start: 0.5446 (OUTLIER) cc_final: 0.4171 (tt0) REVERT: A 152 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7031 (p0) REVERT: A 235 LEU cc_start: 0.7928 (tp) cc_final: 0.7489 (mp) REVERT: A 242 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6582 (mmm-85) REVERT: A 286 MET cc_start: 0.7738 (tpt) cc_final: 0.7066 (mtt) REVERT: A 457 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6074 (tp) outliers start: 13 outliers final: 5 residues processed: 61 average time/residue: 0.0471 time to fit residues: 3.7610 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.195896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164140 restraints weight = 3345.708| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.85 r_work: 0.3771 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3044 Z= 0.133 Angle : 0.626 7.386 4174 Z= 0.292 Chirality : 0.040 0.134 512 Planarity : 0.005 0.032 520 Dihedral : 3.709 13.185 433 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.67 % Allowed : 17.00 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.44), residues: 400 helix: 1.83 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.47 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.010 0.001 TYR A 421 PHE 0.026 0.001 PHE A 163 TRP 0.005 0.001 TRP A 315 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 3044) covalent geometry : angle 0.62640 / 0.29 ( 4174) hydrogen bonds : bond 0.03484 / 2.31 ( 252) hydrogen bonds : angle 3.94418 / 2.89 ( 741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.107 Fit side-chains REVERT: A 26 GLN cc_start: 0.5372 (OUTLIER) cc_final: 0.4176 (tt0) REVERT: A 152 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6996 (p0) REVERT: A 235 LEU cc_start: 0.7924 (tp) cc_final: 0.7483 (mp) REVERT: A 242 ARG cc_start: 0.6817 (mmm-85) cc_final: 0.6530 (mmm-85) REVERT: A 286 MET cc_start: 0.7746 (tpt) cc_final: 0.7064 (mtt) REVERT: A 419 SER cc_start: 0.8356 (t) cc_final: 0.7923 (m) REVERT: A 457 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6203 (tp) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.0479 time to fit residues: 3.6355 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.194818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162900 restraints weight = 3364.712| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.85 r_work: 0.3760 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3044 Z= 0.142 Angle : 0.628 7.556 4174 Z= 0.294 Chirality : 0.040 0.131 512 Planarity : 0.005 0.032 520 Dihedral : 3.716 12.999 433 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.00 % Allowed : 19.33 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.44), residues: 400 helix: 1.84 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.55 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.013 0.001 TYR A 421 PHE 0.027 0.002 PHE A 163 TRP 0.004 0.001 TRP A 331 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 3044) covalent geometry : angle 0.62797 / 0.29 ( 4174) hydrogen bonds : bond 0.03555 / 2.36 ( 252) hydrogen bonds : angle 3.94592 / 2.89 ( 741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.110 Fit side-chains REVERT: A 26 GLN cc_start: 0.5456 (OUTLIER) cc_final: 0.4157 (tt0) REVERT: A 152 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7024 (p0) REVERT: A 235 LEU cc_start: 0.7936 (tp) cc_final: 0.7464 (mp) REVERT: A 286 MET cc_start: 0.7712 (tpt) cc_final: 0.7044 (mtt) REVERT: A 419 SER cc_start: 0.8371 (t) cc_final: 0.7930 (m) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.0414 time to fit residues: 3.3911 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.195316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163443 restraints weight = 3382.230| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.86 r_work: 0.3763 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3044 Z= 0.133 Angle : 0.621 7.033 4174 Z= 0.290 Chirality : 0.040 0.124 512 Planarity : 0.005 0.032 520 Dihedral : 3.695 13.066 433 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.00 % Allowed : 19.67 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.44), residues: 400 helix: 1.91 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.54 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.011 0.001 TYR A 421 PHE 0.028 0.002 PHE A 163 TRP 0.004 0.001 TRP A 315 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 3044) covalent geometry : angle 0.62134 / 0.29 ( 4174) hydrogen bonds : bond 0.03406 / 2.26 ( 252) hydrogen bonds : angle 3.89043 / 2.85 ( 741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.064 Fit side-chains REVERT: A 26 GLN cc_start: 0.5424 (OUTLIER) cc_final: 0.4235 (tt0) REVERT: A 34 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7598 (mt) REVERT: A 152 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7055 (p0) REVERT: A 185 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: A 235 LEU cc_start: 0.7940 (tp) cc_final: 0.7442 (mp) REVERT: A 286 MET cc_start: 0.7710 (tpt) cc_final: 0.7030 (mtt) REVERT: A 419 SER cc_start: 0.8363 (t) cc_final: 0.7913 (m) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.0311 time to fit residues: 2.3628 Evaluate side-chains 59 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.189698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156287 restraints weight = 3371.509| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.92 r_work: 0.3696 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3044 Z= 0.128 Angle : 0.616 6.724 4174 Z= 0.288 Chirality : 0.039 0.123 512 Planarity : 0.005 0.031 520 Dihedral : 3.681 13.197 433 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.33 % Allowed : 20.67 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.44), residues: 400 helix: 1.97 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.58 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.011 0.001 TYR A 421 PHE 0.025 0.002 PHE A 163 TRP 0.004 0.001 TRP A 315 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 3044) covalent geometry : angle 0.61563 / 0.29 ( 4174) hydrogen bonds : bond 0.03319 / 2.20 ( 252) hydrogen bonds : angle 3.88293 / 2.85 ( 741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.107 Fit side-chains REVERT: A 26 GLN cc_start: 0.5275 (OUTLIER) cc_final: 0.4039 (tt0) REVERT: A 34 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 152 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6986 (p0) REVERT: A 235 LEU cc_start: 0.7782 (tp) cc_final: 0.7301 (mp) REVERT: A 286 MET cc_start: 0.7720 (tpt) cc_final: 0.6980 (mtt) REVERT: A 419 SER cc_start: 0.8322 (t) cc_final: 0.7829 (m) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.0487 time to fit residues: 3.6958 Evaluate side-chains 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.188759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155456 restraints weight = 3357.129| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.91 r_work: 0.3680 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3044 Z= 0.137 Angle : 0.627 7.024 4174 Z= 0.293 Chirality : 0.040 0.126 512 Planarity : 0.005 0.031 520 Dihedral : 3.690 13.119 433 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.00 % Allowed : 20.67 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.44), residues: 400 helix: 1.97 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.60 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.012 0.001 TYR A 421 PHE 0.027 0.002 PHE A 163 TRP 0.005 0.001 TRP A 315 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 3044) covalent geometry : angle 0.62668 / 0.29 ( 4174) hydrogen bonds : bond 0.03440 / 2.27 ( 252) hydrogen bonds : angle 3.91645 / 2.88 ( 741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.132 Fit side-chains REVERT: A 26 GLN cc_start: 0.5329 (OUTLIER) cc_final: 0.4012 (tt0) REVERT: A 34 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7523 (mt) REVERT: A 152 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6994 (p0) REVERT: A 235 LEU cc_start: 0.7797 (tp) cc_final: 0.7316 (mp) REVERT: A 286 MET cc_start: 0.7732 (tpt) cc_final: 0.6985 (mtt) REVERT: A 419 SER cc_start: 0.8338 (t) cc_final: 0.7832 (m) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.0545 time to fit residues: 3.9575 Evaluate side-chains 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.194677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162893 restraints weight = 3367.395| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.85 r_work: 0.3763 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3044 Z= 0.140 Angle : 0.628 7.026 4174 Z= 0.295 Chirality : 0.040 0.130 512 Planarity : 0.005 0.032 520 Dihedral : 3.701 13.237 433 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.00 % Allowed : 20.33 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.44), residues: 400 helix: 1.94 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.63 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.013 0.001 TYR A 421 PHE 0.026 0.002 PHE A 163 TRP 0.005 0.001 TRP A 331 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 3044) covalent geometry : angle 0.62837 / 0.29 ( 4174) hydrogen bonds : bond 0.03467 / 2.29 ( 252) hydrogen bonds : angle 3.92537 / 2.89 ( 741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.107 Fit side-chains REVERT: A 26 GLN cc_start: 0.5331 (OUTLIER) cc_final: 0.4085 (tt0) REVERT: A 34 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 152 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7041 (p0) REVERT: A 235 LEU cc_start: 0.7914 (tp) cc_final: 0.7415 (mp) REVERT: A 286 MET cc_start: 0.7730 (tpt) cc_final: 0.6971 (mtt) REVERT: A 327 MET cc_start: 0.8508 (ttm) cc_final: 0.8257 (mtm) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.0525 time to fit residues: 3.8915 Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156531 restraints weight = 3306.693| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.90 r_work: 0.3702 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3044 Z= 0.128 Angle : 0.615 6.975 4174 Z= 0.287 Chirality : 0.039 0.122 512 Planarity : 0.005 0.031 520 Dihedral : 3.667 13.534 433 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.00 % Allowed : 20.00 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.44), residues: 400 helix: 2.02 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.54 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.011 0.001 TYR A 421 PHE 0.026 0.002 PHE A 163 TRP 0.004 0.001 TRP A 331 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 3044) covalent geometry : angle 0.61450 / 0.29 ( 4174) hydrogen bonds : bond 0.03310 / 2.18 ( 252) hydrogen bonds : angle 3.88332 / 2.86 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 830.68 seconds wall clock time: 14 minutes 57.31 seconds (897.31 seconds total)