Starting phenix.real_space_refine on Wed Mar 5 17:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jri_61756/03_2025/9jri_61756_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jri_61756/03_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_61756/03_2025/9jri_61756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jri_61756/03_2025/9jri_61756.map" model { file = "/net/cci-nas-00/data/ceres_data/9jri_61756/03_2025/9jri_61756_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jri_61756/03_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-5624/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: 2.78, per 1000 atoms: 0.89 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: 0.85 Conformation dependent library (CDL) restraints added in 344.1 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: 0.28 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: 0.81 Time building geometry restraints manager: 0.96 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: 0.750 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- 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= 0.360 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 *********************** 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 : 0.313 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1744 time to fit residues: 9.6448 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 : 0.343 ------------------------------------------------------------------------------- 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: 4.97 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= 0.193 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 *********************** 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 : 0.449 Fit side-chains REVERT: A 45 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: A 162 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 377 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8856 (mm-40) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 0.1956 time to fit residues: 12.5045 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 : 0.391 ------------------------------------------------------------------------------- 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: 0.0470 chunk 9 optimal weight: 0.6980 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: 0.2544 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.167054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142455 restraints weight = 3853.465| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.94 r_work: 0.3562 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3221 Z= 0.153 Angle : 0.545 7.687 4390 Z= 0.267 Chirality : 0.037 0.120 509 Planarity : 0.004 0.057 523 Dihedral : 15.343 164.161 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.14 % Allowed : 25.08 % 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: 1.68 (0.44), residues: 379 helix: 1.66 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.56 (0.85), 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 0.020 0.001 PHE A 372 TYR 0.021 0.001 TYR A 366 ARG 0.002 0.000 ARG A 61 *********************** 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 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.325 Fit side-chains REVERT: A 111 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7194 (pp) REVERT: A 127 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8572 (t) REVERT: A 151 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8470 (tpp-160) REVERT: A 326 PHE cc_start: 0.6937 (m-10) cc_final: 0.6666 (m-10) REVERT: A 371 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 377 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8739 (mm-40) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 0.1727 time to fit residues: 13.1975 Evaluate side-chains 59 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.163490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138610 restraints weight = 3981.465| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.95 r_work: 0.3509 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3221 Z= 0.195 Angle : 0.567 8.106 4390 Z= 0.280 Chirality : 0.039 0.150 509 Planarity : 0.004 0.054 523 Dihedral : 15.264 171.093 452 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.83 % Allowed : 27.79 % Favored : 67.37 % 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: 1.59 (0.43), residues: 379 helix: 1.58 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.44 (0.85), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.013 0.001 HIS A 355 PHE 0.029 0.001 PHE A 372 TYR 0.017 0.002 TYR A 149 ARG 0.003 0.000 ARG A 61 *********************** 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 62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.321 Fit side-chains REVERT: A 111 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7219 (pp) REVERT: A 127 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8664 (t) REVERT: A 327 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7188 (t) REVERT: A 371 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7697 (mp) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.1828 time to fit residues: 12.8487 Evaluate side-chains 55 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 327 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 371 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: 0.0970 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.162898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137381 restraints weight = 4007.743| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.97 r_work: 0.3492 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3221 Z= 0.215 Angle : 0.591 8.178 4390 Z= 0.291 Chirality : 0.040 0.181 509 Planarity : 0.004 0.054 523 Dihedral : 15.202 172.720 452 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.04 % Allowed : 25.98 % 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: 1.43 (0.43), residues: 379 helix: 1.48 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.56 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 355 PHE 0.024 0.002 PHE A 372 TYR 0.018 0.001 TYR A 438 ARG 0.002 0.000 ARG A 151 *********************** 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 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.320 Fit side-chains REVERT: A 127 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8727 (t) REVERT: A 162 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 255 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6457 (mm) REVERT: A 327 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7276 (t) REVERT: A 371 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7758 (mp) outliers start: 20 outliers final: 12 residues processed: 61 average time/residue: 0.1730 time to fit residues: 12.6720 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 : 0.313 ------------------------------------------------------------------------------- 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 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 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 375 SER Chi-restraints excluded: chain A residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.162510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136992 restraints weight = 4044.296| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.04 r_work: 0.3493 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3221 Z= 0.229 Angle : 0.595 8.444 4390 Z= 0.292 Chirality : 0.039 0.134 509 Planarity : 0.004 0.054 523 Dihedral : 15.161 172.438 452 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.74 % Allowed : 26.28 % 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: 1.49 (0.43), residues: 379 helix: 1.52 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -1.55 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.010 0.001 HIS A 355 PHE 0.022 0.001 PHE A 372 TYR 0.018 0.001 TYR A 438 ARG 0.006 0.000 ARG A 61 *********************** 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 65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.323 Fit side-chains REVERT: A 127 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8736 (t) REVERT: A 162 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 255 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6448 (mm) REVERT: A 327 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7255 (t) REVERT: A 371 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7835 (mp) outliers start: 19 outliers final: 13 residues processed: 62 average time/residue: 0.1755 time to fit residues: 12.9495 Evaluate side-chains 62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 411 LYS Chi-restraints excluded: chain A residue 426 LEU 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: 0.7980 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 7 optimal weight: 0.2980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.163502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138212 restraints weight = 3966.203| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.93 r_work: 0.3475 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1377 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= 0.173 Angle : 0.573 8.110 4390 Z= 0.278 Chirality : 0.038 0.134 509 Planarity : 0.004 0.052 523 Dihedral : 15.097 172.664 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.04 % Allowed : 26.59 % Favored : 67.37 % 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: 1.73 (0.43), residues: 379 helix: 1.69 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.46 (0.86), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.003 0.000 HIS A 355 PHE 0.020 0.001 PHE A 372 TYR 0.014 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 *********************** 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 67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.343 Fit side-chains REVERT: A 38 MET cc_start: 0.8640 (tpp) cc_final: 0.8405 (mtp) REVERT: A 127 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 139 TYR cc_start: 0.8887 (t80) cc_final: 0.8442 (t80) REVERT: A 162 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 327 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7184 (t) REVERT: A 371 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7804 (mp) outliers start: 20 outliers final: 15 residues processed: 62 average time/residue: 0.1601 time to fit residues: 12.0832 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 : 0.341 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.163573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138380 restraints weight = 3980.187| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.93 r_work: 0.3511 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1435 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= 0.179 Angle : 0.580 7.948 4390 Z= 0.280 Chirality : 0.038 0.134 509 Planarity : 0.004 0.052 523 Dihedral : 15.084 172.232 452 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.74 % Allowed : 27.19 % 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: 1.80 (0.43), residues: 379 helix: 1.73 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -1.50 (0.87), residues: 64 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 0.019 0.001 PHE A 372 TYR 0.014 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 *********************** 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 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.315 Fit side-chains REVERT: A 38 MET cc_start: 0.8629 (tpp) cc_final: 0.8405 (mtp) REVERT: A 127 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 139 TYR cc_start: 0.8896 (t80) cc_final: 0.8678 (t80) REVERT: A 162 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 255 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6416 (mm) REVERT: A 327 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7206 (t) REVERT: A 371 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7807 (mp) outliers start: 19 outliers final: 13 residues processed: 63 average time/residue: 0.1632 time to fit residues: 12.4964 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 : 0.347 ------------------------------------------------------------------------------- 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 255 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 365 CYS Chi-restraints excluded: chain A residue 371 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137150 restraints weight = 3980.156| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.93 r_work: 0.3512 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3221 Z= 0.206 Angle : 0.602 8.130 4390 Z= 0.295 Chirality : 0.039 0.135 509 Planarity : 0.004 0.053 523 Dihedral : 15.107 171.590 452 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.34 % Allowed : 26.89 % 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: 1.73 (0.43), residues: 379 helix: 1.67 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -1.48 (0.89), residues: 63 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 0.019 0.001 PHE A 372 TYR 0.016 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 *********************** 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 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.334 Fit side-chains REVERT: A 38 MET cc_start: 0.8699 (tpp) cc_final: 0.8420 (mtp) REVERT: A 127 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 139 TYR cc_start: 0.8905 (t80) cc_final: 0.8689 (t80) REVERT: A 162 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 255 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6430 (mm) REVERT: A 327 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7169 (t) REVERT: A 371 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7827 (mp) outliers start: 21 outliers final: 13 residues processed: 66 average time/residue: 0.1477 time to fit residues: 12.0926 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 : 0.333 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.163600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138109 restraints weight = 3889.496| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.96 r_work: 0.3492 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3221 Z= 0.207 Angle : 0.612 8.057 4390 Z= 0.298 Chirality : 0.039 0.133 509 Planarity : 0.004 0.053 523 Dihedral : 15.092 171.041 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.74 % Allowed : 28.10 % Favored : 66.16 % 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: 1.73 (0.43), residues: 379 helix: 1.67 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -1.49 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.019 0.001 PHE A 372 TYR 0.017 0.001 TYR A 438 ARG 0.005 0.000 ARG A 61 ********************** 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 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.325 Fit side-chains REVERT: A 127 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8729 (t) REVERT: A 139 TYR cc_start: 0.8897 (t80) cc_final: 0.8685 (t80) REVERT: A 162 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 255 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6424 (mm) REVERT: A 327 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7146 (t) REVERT: A 371 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7869 (mp) outliers start: 19 outliers final: 14 residues processed: 65 average time/residue: 0.1801 time to fit residues: 14.1372 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 : 0.324 ------------------------------------------------------------------------------- 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 199 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.164084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138241 restraints weight = 3959.973| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.00 r_work: 0.3513 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1530 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= 0.199 Angle : 0.612 8.079 4390 Z= 0.295 Chirality : 0.039 0.132 509 Planarity : 0.004 0.052 523 Dihedral : 15.087 170.717 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: 1.82 (0.43), residues: 379 helix: 1.74 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -1.47 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.52 seconds wall clock time: 36 minutes 14.53 seconds (2174.53 seconds total)