Starting phenix.real_space_refine on Fri May 9 16:21:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jri_61756/05_2025/9jri_61756_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jri_61756/05_2025/9jri_61756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jri_61756/05_2025/9jri_61756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jri_61756/05_2025/9jri_61756.map" model { file = "/net/cci-nas-00/data/ceres_data/9jri_61756/05_2025/9jri_61756_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jri_61756/05_2025/9jri_61756_neut.cif" } resolution = 3.43 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= 0.001 sd= 0.066 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 10 5.16 5 C 2093 2.51 5 N 515 2.21 5 O 514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3132 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3099 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 12, 'TRANS': 372} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'C2F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.85 Number of scatterers: 3132 At special positions: 0 Unit cell: (66, 64, 78, 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 10 16.00 O 514 8.00 N 515 7.00 C 2093 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: 0.87 Conformation dependent library (CDL) restraints added in 367.1 milliseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB C2F A 701 " Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.716A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.944A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.715A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.516A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.608A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.628A pdb=" N TYR A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.940A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 264 through 294 removed outlier: 3.816A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.746A pdb=" N HIS A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 389 removed outlier: 3.767A pdb=" N LEU A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.733A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.695A pdb=" N PHE A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 453 234 hydrogen bonds defined for protein. 702 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: 0.76 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 436 1.30 - 1.43: 977 1.43 - 1.56: 1792 1.56 - 1.69: 0 1.69 - 1.82: 16 Bond restraints: 3221 Sorted by residual: bond pdb=" C8A C2F A 701 " pdb=" N8 C2F A 701 " ideal model delta sigma weight residual 1.344 1.504 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C2 C2F A 701 " pdb=" NA2 C2F A 701 " ideal model delta sigma weight residual 1.345 1.444 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N C2F A 701 " pdb=" C C2F A 701 " ideal model delta sigma weight residual 1.343 1.427 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 C2F A 701 " pdb=" C4A C2F A 701 " ideal model delta sigma weight residual 1.415 1.335 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C6 C2F A 701 " pdb=" N5 C2F A 701 " ideal model delta sigma weight residual 1.452 1.373 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 3216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 4322 3.08 - 6.16: 51 6.16 - 9.24: 15 9.24 - 12.32: 1 12.32 - 15.40: 1 Bond angle restraints: 4390 Sorted by residual: angle pdb=" C15 C2F A 701 " pdb=" N10 C2F A 701 " pdb=" C9 C2F A 701 " ideal model delta sigma weight residual 122.08 106.68 15.40 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C6 C2F A 701 " pdb=" C9 C2F A 701 " pdb=" N10 C2F A 701 " ideal model delta sigma weight residual 109.12 97.21 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.20e+00 angle pdb=" N LEU A 77 " pdb=" CA LEU A 77 " pdb=" C LEU A 77 " ideal model delta sigma weight residual 112.72 109.02 3.70 1.36e+00 5.41e-01 7.42e+00 angle pdb=" CA TYR A 74 " pdb=" CB TYR A 74 " pdb=" CG TYR A 74 " ideal model delta sigma weight residual 113.90 118.71 -4.81 1.80e+00 3.09e-01 7.15e+00 ... (remaining 4385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 1688 26.07 - 52.15: 139 52.15 - 78.22: 12 78.22 - 104.29: 1 104.29 - 130.36: 6 Dihedral angle restraints: 1846 sinusoidal: 713 harmonic: 1133 Sorted by residual: dihedral pdb=" C11 C2F A 701 " pdb=" C6 C2F A 701 " pdb=" N5 C2F A 701 " pdb=" C9 C2F A 701 " ideal model delta sinusoidal sigma weight residual 202.19 71.83 130.36 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C11 C2F A 701 " pdb=" C6 C2F A 701 " pdb=" N5 C2F A 701 " pdb=" C7 C2F A 701 " ideal model delta sinusoidal sigma weight residual 78.30 -48.05 126.35 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" N5 C2F A 701 " pdb=" C6 C2F A 701 " pdb=" C7 C2F A 701 " pdb=" N8 C2F A 701 " ideal model delta sinusoidal sigma weight residual -52.13 73.03 -125.16 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 1843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 320 0.032 - 0.064: 134 0.064 - 0.097: 39 0.097 - 0.129: 14 0.129 - 0.161: 2 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA LEU A 258 " pdb=" N LEU A 258 " pdb=" C LEU A 258 " pdb=" CB LEU A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA LEU A 112 " pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CB LEU A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 506 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 426 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 427 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 145 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 146 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C C2F A 701 " 0.008 2.00e-02 2.50e+03 8.38e-03 1.40e+00 pdb=" C12 C2F A 701 " -0.009 2.00e-02 2.50e+03 pdb=" C13 C2F A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C14 C2F A 701 " -0.003 2.00e-02 2.50e+03 pdb=" C15 C2F A 701 " -0.015 2.00e-02 2.50e+03 pdb=" C16 C2F A 701 " 0.000 2.00e-02 2.50e+03 pdb=" C17 C2F A 701 " 0.000 2.00e-02 2.50e+03 pdb=" N10 C2F A 701 " 0.013 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 47 2.67 - 3.23: 3139 3.23 - 3.79: 5379 3.79 - 4.34: 6550 4.34 - 4.90: 10905 Nonbonded interactions: 26020 Sorted by model distance: nonbonded pdb=" OE1 GLU A 123 " pdb=" O4 C2F A 701 " model vdw 2.119 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" O LEU A 199 " model vdw 2.239 3.040 nonbonded pdb=" OE2 GLU A 123 " pdb=" O4 C2F A 701 " model vdw 2.320 3.040 nonbonded pdb=" OG SER A 271 " pdb=" OD1 ASN A 403 " model vdw 2.340 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O GLN A 377 " model vdw 2.342 3.040 ... (remaining 26015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.420 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.006 0.160 3221 Z= 0.326 Angle : 0.870 15.395 4390 Z= 0.392 Chirality : 0.040 0.161 509 Planarity : 0.006 0.102 523 Dihedral : 19.715 130.361 1118 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.30 % Allowed : 31.42 % Favored : 68.28 % Cbeta Deviations : 0.27 % 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: 1.04 (0.43), residues: 379 helix: 1.15 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -1.27 (0.85), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.017 0.001 PHE A 84 TYR 0.017 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.11713 ( 234) hydrogen bonds : angle 5.76268 ( 702) covalent geometry : bond 0.00648 ( 3221) covalent geometry : angle 0.87023 ( 4390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.307 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1759 time to fit residues: 9.7096 Evaluate side-chains 45 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140121 restraints weight = 3946.548| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.00 r_work: 0.3518 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3221 Z= 0.141 Angle : 0.592 7.837 4390 Z= 0.291 Chirality : 0.038 0.124 509 Planarity : 0.004 0.068 523 Dihedral : 15.538 153.177 452 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.93 % Allowed : 28.10 % Favored : 67.98 % Cbeta Deviations : 0.27 % 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: 1.45 (0.44), residues: 379 helix: 1.48 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.45 (0.86), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.015 0.001 PHE A 84 TYR 0.016 0.001 TYR A 438 ARG 0.004 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 234) hydrogen bonds : angle 4.48647 ( 702) covalent geometry : bond 0.00301 ( 3221) covalent geometry : angle 0.59174 ( 4390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.340 Fit side-chains REVERT: A 45 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: A 162 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 377 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8855 (mm-40) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 0.1777 time to fit residues: 11.4153 Evaluate side-chains 51 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.4980 chunk 28 optimal weight: 0.0270 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 overall best weight: 0.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141922 restraints weight = 3858.732| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.93 r_work: 0.3552 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3221 Z= 0.122 Angle : 0.549 7.723 4390 Z= 0.269 Chirality : 0.037 0.123 509 Planarity : 0.004 0.057 523 Dihedral : 15.368 164.181 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.44 % Allowed : 24.77 % Favored : 69.79 % Cbeta Deviations : 0.27 % 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: 1.66 (0.44), residues: 379 helix: 1.64 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.55 (0.85), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.008 0.001 HIS A 355 PHE 0.018 0.001 PHE A 372 TYR 0.021 0.001 TYR A 366 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 234) hydrogen bonds : angle 4.19617 ( 702) covalent geometry : bond 0.00246 ( 3221) covalent geometry : angle 0.54877 ( 4390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.299 Fit side-chains REVERT: A 111 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7210 (pp) REVERT: A 127 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 326 PHE cc_start: 0.6944 (m-10) cc_final: 0.6717 (m-10) REVERT: A 371 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 377 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8755 (mm-40) outliers start: 18 outliers final: 9 residues processed: 63 average time/residue: 0.1668 time to fit residues: 12.5896 Evaluate side-chains 58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138046 restraints weight = 3994.741| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.95 r_work: 0.3525 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3221 Z= 0.147 Angle : 0.576 8.122 4390 Z= 0.283 Chirality : 0.039 0.160 509 Planarity : 0.004 0.055 523 Dihedral : 15.288 169.574 452 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.74 % Allowed : 26.59 % Favored : 67.67 % Cbeta Deviations : 0.27 % 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: 1.51 (0.43), residues: 379 helix: 1.54 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.55 (0.85), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 355 PHE 0.029 0.001 PHE A 372 TYR 0.018 0.002 TYR A 149 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 234) hydrogen bonds : angle 4.14144 ( 702) covalent geometry : bond 0.00325 ( 3221) covalent geometry : angle 0.57648 ( 4390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.326 Fit side-chains REVERT: A 127 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 162 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 327 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7185 (t) REVERT: A 371 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7703 (mp) outliers start: 19 outliers final: 10 residues processed: 60 average time/residue: 0.1562 time to fit residues: 11.4102 Evaluate side-chains 57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141207 restraints weight = 3958.208| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.92 r_work: 0.3508 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3221 Z= 0.118 Angle : 0.552 7.134 4390 Z= 0.270 Chirality : 0.038 0.130 509 Planarity : 0.004 0.052 523 Dihedral : 15.146 173.357 452 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.23 % Allowed : 27.19 % Favored : 68.58 % Cbeta Deviations : 0.27 % 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: 1.75 (0.43), residues: 379 helix: 1.69 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.42 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.009 0.001 HIS A 355 PHE 0.024 0.001 PHE A 372 TYR 0.012 0.001 TYR A 149 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 234) hydrogen bonds : angle 4.00493 ( 702) covalent geometry : bond 0.00241 ( 3221) covalent geometry : angle 0.55226 ( 4390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.351 Fit side-chains REVERT: A 127 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8619 (t) REVERT: A 162 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 326 PHE cc_start: 0.7008 (m-10) cc_final: 0.6742 (m-10) REVERT: A 327 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7175 (t) REVERT: A 371 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7695 (mp) outliers start: 14 outliers final: 8 residues processed: 58 average time/residue: 0.1769 time to fit residues: 12.2333 Evaluate side-chains 60 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135797 restraints weight = 4053.434| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.03 r_work: 0.3463 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3221 Z= 0.183 Angle : 0.625 8.059 4390 Z= 0.307 Chirality : 0.041 0.134 509 Planarity : 0.004 0.053 523 Dihedral : 15.213 172.083 452 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.53 % Allowed : 26.89 % Favored : 68.58 % Cbeta Deviations : 0.27 % 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: 1.44 (0.43), residues: 379 helix: 1.49 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.60 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 25 HIS 0.003 0.000 HIS A 355 PHE 0.022 0.002 PHE A 372 TYR 0.021 0.002 TYR A 438 ARG 0.006 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 234) hydrogen bonds : angle 4.13128 ( 702) covalent geometry : bond 0.00421 ( 3221) covalent geometry : angle 0.62489 ( 4390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.326 Fit side-chains REVERT: A 127 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 162 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 255 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6438 (mm) REVERT: A 282 TYR cc_start: 0.8174 (m-10) cc_final: 0.7922 (m-10) REVERT: A 326 PHE cc_start: 0.7166 (m-10) cc_final: 0.6905 (m-10) REVERT: A 327 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7274 (t) REVERT: A 371 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 377 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8623 (mm-40) outliers start: 15 outliers final: 9 residues processed: 61 average time/residue: 0.1750 time to fit residues: 12.7800 Evaluate side-chains 60 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 411 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.162072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137322 restraints weight = 3960.992| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.92 r_work: 0.3518 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3221 Z= 0.136 Angle : 0.587 7.994 4390 Z= 0.286 Chirality : 0.039 0.135 509 Planarity : 0.004 0.053 523 Dihedral : 15.116 172.529 452 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.44 % Allowed : 27.49 % Favored : 67.07 % Cbeta Deviations : 0.27 % 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: 1.67 (0.43), residues: 379 helix: 1.63 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.43 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.011 0.001 HIS A 355 PHE 0.020 0.001 PHE A 372 TYR 0.016 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 234) hydrogen bonds : angle 4.02203 ( 702) covalent geometry : bond 0.00296 ( 3221) covalent geometry : angle 0.58725 ( 4390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.337 Fit side-chains REVERT: A 38 MET cc_start: 0.8629 (tpp) cc_final: 0.8410 (mtp) REVERT: A 127 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8699 (t) REVERT: A 139 TYR cc_start: 0.8891 (t80) cc_final: 0.8442 (t80) REVERT: A 162 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 326 PHE cc_start: 0.7086 (m-10) cc_final: 0.6848 (m-10) REVERT: A 327 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7151 (t) REVERT: A 371 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7878 (mp) outliers start: 18 outliers final: 13 residues processed: 61 average time/residue: 0.1634 time to fit residues: 12.2414 Evaluate side-chains 62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136056 restraints weight = 3996.943| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.99 r_work: 0.3470 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3221 Z= 0.162 Angle : 0.608 8.039 4390 Z= 0.297 Chirality : 0.040 0.133 509 Planarity : 0.004 0.054 523 Dihedral : 15.165 171.422 452 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.65 % Allowed : 26.59 % Favored : 66.77 % Cbeta Deviations : 0.27 % 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: 1.50 (0.43), residues: 379 helix: 1.53 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.59 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 25 HIS 0.002 0.000 HIS A 355 PHE 0.019 0.001 PHE A 372 TYR 0.019 0.002 TYR A 438 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 234) hydrogen bonds : angle 4.07553 ( 702) covalent geometry : bond 0.00369 ( 3221) covalent geometry : angle 0.60815 ( 4390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.353 Fit side-chains REVERT: A 38 MET cc_start: 0.8759 (tpp) cc_final: 0.8462 (mtp) REVERT: A 127 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8763 (t) REVERT: A 139 TYR cc_start: 0.8911 (t80) cc_final: 0.8483 (t80) REVERT: A 162 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 255 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6455 (mm) REVERT: A 282 TYR cc_start: 0.8237 (m-10) cc_final: 0.7947 (m-10) REVERT: A 326 PHE cc_start: 0.7208 (m-10) cc_final: 0.6984 (m-10) REVERT: A 327 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7263 (t) REVERT: A 371 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7889 (mp) outliers start: 22 outliers final: 14 residues processed: 66 average time/residue: 0.1504 time to fit residues: 12.1880 Evaluate side-chains 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.0370 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136824 restraints weight = 3983.659| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.91 r_work: 0.3512 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3221 Z= 0.137 Angle : 0.586 8.069 4390 Z= 0.287 Chirality : 0.039 0.133 509 Planarity : 0.004 0.053 523 Dihedral : 15.105 171.328 452 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.04 % Allowed : 26.89 % Favored : 67.07 % Cbeta Deviations : 0.27 % 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: 1.65 (0.43), residues: 379 helix: 1.61 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -1.50 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.012 0.001 HIS A 355 PHE 0.019 0.001 PHE A 372 TYR 0.016 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 234) hydrogen bonds : angle 3.99784 ( 702) covalent geometry : bond 0.00299 ( 3221) covalent geometry : angle 0.58568 ( 4390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.314 Fit side-chains REVERT: A 127 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8707 (t) REVERT: A 162 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 326 PHE cc_start: 0.7087 (m-10) cc_final: 0.6846 (m-10) REVERT: A 327 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7152 (t) REVERT: A 371 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7847 (mp) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.1691 time to fit residues: 12.6197 Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137720 restraints weight = 3877.592| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.90 r_work: 0.3501 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3221 Z= 0.128 Angle : 0.576 7.917 4390 Z= 0.281 Chirality : 0.039 0.132 509 Planarity : 0.004 0.053 523 Dihedral : 15.100 171.259 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.04 % Allowed : 27.49 % Favored : 66.47 % Cbeta Deviations : 0.27 % 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: 1.77 (0.43), residues: 379 helix: 1.73 (0.27), residues: 314 sheet: None (None), residues: 0 loop : -1.55 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.019 0.001 PHE A 372 TYR 0.033 0.002 TYR A 139 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 234) hydrogen bonds : angle 3.96228 ( 702) covalent geometry : bond 0.00276 ( 3221) covalent geometry : angle 0.57604 ( 4390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.314 Fit side-chains REVERT: A 38 MET cc_start: 0.8679 (ttm) cc_final: 0.8184 (ttm) REVERT: A 127 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 162 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 326 PHE cc_start: 0.7044 (m-10) cc_final: 0.6815 (m-10) REVERT: A 327 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.7116 (t) REVERT: A 371 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7830 (mp) outliers start: 20 outliers final: 16 residues processed: 63 average time/residue: 0.1572 time to fit residues: 12.0247 Evaluate side-chains 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.160609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135167 restraints weight = 3995.061| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.95 r_work: 0.3433 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3221 Z= 0.157 Angle : 0.607 8.101 4390 Z= 0.300 Chirality : 0.040 0.131 509 Planarity : 0.004 0.053 523 Dihedral : 15.138 170.451 452 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.65 % Allowed : 26.28 % Favored : 67.07 % Cbeta Deviations : 0.27 % 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: 1.67 (0.42), residues: 379 helix: 1.64 (0.27), residues: 315 sheet: None (None), residues: 0 loop : -1.51 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.016 0.002 HIS A 355 PHE 0.018 0.001 PHE A 372 TYR 0.018 0.002 TYR A 438 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 234) hydrogen bonds : angle 4.01168 ( 702) covalent geometry : bond 0.00355 ( 3221) covalent geometry : angle 0.60730 ( 4390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.26 seconds wall clock time: 35 minutes 15.75 seconds (2115.75 seconds total)