Starting phenix.real_space_refine on Mon Feb 10 23:01:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esa_28573/02_2025/8esa_28573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esa_28573/02_2025/8esa_28573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8esa_28573/02_2025/8esa_28573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esa_28573/02_2025/8esa_28573.map" model { file = "/net/cci-nas-00/data/ceres_data/8esa_28573/02_2025/8esa_28573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esa_28573/02_2025/8esa_28573.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 72 atoms to isotropic. 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 14 5.16 5 C 1970 2.51 5 N 563 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3140 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2223 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 828 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 89 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 2.74, per 1000 atoms: 0.87 Number of scatterers: 3140 At special positions: 0 Unit cell: (84.15, 65.45, 67.15, 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 14 16.00 O 593 8.00 N 563 7.00 C 1970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 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: 0.68 Conformation dependent library (CDL) restraints added in 384.6 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 17.4% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 56 through 85 removed outlier: 3.820A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.699A pdb=" N HIS A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.511A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.965A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 101 " --> pdb=" O MET A 5 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 99 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 94 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 118 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN A 96 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR A 116 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET A 98 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A 114 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 100 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY A 112 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP A 102 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 4.072A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 190 removed outlier: 4.072A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.801A pdb=" N GLU A 222 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.981A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 63 " --> pdb=" O SER B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 134 hydrogen bonds defined for protein. 354 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: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1049 1.34 - 1.46: 794 1.46 - 1.58: 1365 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 3228 Sorted by residual: bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.506 1.468 0.038 3.90e-02 6.57e+02 9.41e-01 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.468 0.038 3.90e-02 6.57e+02 9.38e-01 bond pdb=" CB VAL C 2 " pdb=" CG2 VAL C 2 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.64e-01 bond pdb=" CB ARG A 35 " pdb=" CG ARG A 35 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.39e-01 bond pdb=" CG PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 5.95e-01 ... (remaining 3223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 4137 0.97 - 1.95: 195 1.95 - 2.92: 35 2.92 - 3.89: 7 3.89 - 4.86: 1 Bond angle restraints: 4375 Sorted by residual: angle pdb=" C CYS A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta sigma weight residual 120.42 117.04 3.38 1.42e+00 4.96e-01 5.66e+00 angle pdb=" CA TYR A 159 " pdb=" CB TYR A 159 " pdb=" CG TYR A 159 " ideal model delta sigma weight residual 113.90 110.50 3.40 1.80e+00 3.09e-01 3.56e+00 angle pdb=" C GLN A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 120.68 118.37 2.31 1.70e+00 3.46e-01 1.85e+00 angle pdb=" C THR A 163 " pdb=" N CYS A 164 " pdb=" CA CYS A 164 " ideal model delta sigma weight residual 120.29 118.39 1.90 1.42e+00 4.96e-01 1.79e+00 angle pdb=" CA CYS A 164 " pdb=" C CYS A 164 " pdb=" N VAL A 165 " ideal model delta sigma weight residual 117.39 118.94 -1.55 1.24e+00 6.50e-01 1.57e+00 ... (remaining 4370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 1642 15.45 - 30.89: 200 30.89 - 46.33: 45 46.33 - 61.78: 12 61.78 - 77.22: 5 Dihedral angle restraints: 1904 sinusoidal: 788 harmonic: 1116 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ARG B 81 " pdb=" CB ARG B 81 " pdb=" CG ARG B 81 " pdb=" CD ARG B 81 " ideal model delta sinusoidal sigma weight residual -60.00 -111.49 51.49 3 1.50e+01 4.44e-03 9.02e+00 dihedral pdb=" CA ARG A 256 " pdb=" CB ARG A 256 " pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " ideal model delta sinusoidal sigma weight residual -180.00 -129.33 -50.67 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 245 0.028 - 0.056: 129 0.056 - 0.084: 45 0.084 - 0.111: 17 0.111 - 0.139: 8 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CB VAL A 165 " pdb=" CA VAL A 165 " pdb=" CG1 VAL A 165 " pdb=" CG2 VAL A 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 441 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C LEU A 160 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 161 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 161 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C GLU A 161 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU A 161 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A 162 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 49 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.38e-01 pdb=" N PRO A 50 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.014 5.00e-02 4.00e+02 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 588 2.77 - 3.31: 2685 3.31 - 3.84: 4624 3.84 - 4.37: 5574 4.37 - 4.90: 10145 Nonbonded interactions: 23616 Sorted by model distance: nonbonded pdb=" OH TYR A 59 " pdb=" OH TYR A 171 " model vdw 2.243 3.040 nonbonded pdb=" O GLN A 255 " pdb=" NH2 ARG A 273 " model vdw 2.351 3.120 nonbonded pdb=" O SER A 207 " pdb=" OG SER A 207 " model vdw 2.391 3.040 nonbonded pdb=" OE2 GLU B 36 " pdb=" NH1 ARG B 81 " model vdw 2.415 3.120 nonbonded pdb=" NH2 ARG A 14 " pdb=" O GLU A 19 " model vdw 2.459 3.120 ... (remaining 23611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 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: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3228 Z= 0.256 Angle : 0.493 4.865 4375 Z= 0.260 Chirality : 0.041 0.139 444 Planarity : 0.004 0.028 571 Dihedral : 14.826 77.222 1176 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.43), residues: 376 helix: 1.18 (0.60), residues: 66 sheet: -0.23 (0.52), residues: 110 loop : -1.58 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 244 HIS 0.003 0.001 HIS B 84 PHE 0.014 0.002 PHE B 56 TYR 0.010 0.001 TYR A 159 ARG 0.005 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.372 Fit side-chains REVERT: A 110 LEU cc_start: 0.7718 (tt) cc_final: 0.7508 (tt) REVERT: A 154 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6901 (pt0) REVERT: B 45 ARG cc_start: 0.7243 (ttp80) cc_final: 0.5821 (mmt90) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2159 time to fit residues: 13.1732 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.166936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131436 restraints weight = 3685.486| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.29 r_work: 0.3367 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3228 Z= 0.216 Angle : 0.528 5.914 4375 Z= 0.281 Chirality : 0.042 0.151 444 Planarity : 0.004 0.025 571 Dihedral : 4.202 15.873 429 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.60 % Allowed : 5.72 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.43), residues: 376 helix: 0.93 (0.61), residues: 72 sheet: -0.49 (0.47), residues: 129 loop : -1.23 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 204 HIS 0.003 0.001 HIS A 93 PHE 0.012 0.002 PHE B 56 TYR 0.013 0.001 TYR A 159 ARG 0.004 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.338 Fit side-chains REVERT: A 110 LEU cc_start: 0.7954 (tt) cc_final: 0.7633 (tt) REVERT: A 154 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7163 (pt0) REVERT: A 157 ARG cc_start: 0.8157 (ttt-90) cc_final: 0.7782 (ptm-80) REVERT: A 159 TYR cc_start: 0.8207 (t80) cc_final: 0.7904 (t80) REVERT: A 222 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: B 45 ARG cc_start: 0.7910 (ttp80) cc_final: 0.5822 (mmt90) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.2001 time to fit residues: 12.2963 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.161947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126108 restraints weight = 3645.031| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.38 r_work: 0.3317 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3228 Z= 0.263 Angle : 0.513 5.141 4375 Z= 0.273 Chirality : 0.042 0.149 444 Planarity : 0.004 0.026 571 Dihedral : 4.200 16.276 429 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.90 % Allowed : 9.04 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 376 helix: 1.05 (0.60), residues: 72 sheet: -0.64 (0.45), residues: 135 loop : -1.17 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 204 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.002 PHE B 56 TYR 0.010 0.001 TYR B 63 ARG 0.002 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.337 Fit side-chains REVERT: A 110 LEU cc_start: 0.7926 (tt) cc_final: 0.7551 (tt) REVERT: A 154 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7173 (pt0) REVERT: A 157 ARG cc_start: 0.8097 (ttt-90) cc_final: 0.7751 (ptm-80) REVERT: A 222 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 256 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8569 (mtt180) REVERT: B 45 ARG cc_start: 0.7956 (ttp80) cc_final: 0.5756 (mmt90) outliers start: 3 outliers final: 0 residues processed: 49 average time/residue: 0.1987 time to fit residues: 11.5539 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 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 = 0.3906 r_free = 0.3906 target = 0.162231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126260 restraints weight = 3721.955| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.41 r_work: 0.3332 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3228 Z= 0.247 Angle : 0.511 6.265 4375 Z= 0.268 Chirality : 0.041 0.136 444 Planarity : 0.003 0.027 571 Dihedral : 4.119 16.369 429 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.11 % Allowed : 10.54 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.42), residues: 376 helix: 1.26 (0.60), residues: 72 sheet: -0.70 (0.44), residues: 140 loop : -1.08 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 204 HIS 0.003 0.001 HIS B 84 PHE 0.013 0.002 PHE B 56 TYR 0.023 0.001 TYR A 159 ARG 0.002 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.339 Fit side-chains REVERT: A 77 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7620 (t0) REVERT: A 110 LEU cc_start: 0.7955 (tt) cc_final: 0.7563 (tt) REVERT: A 154 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7219 (pt0) REVERT: A 157 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7740 (ptm-80) REVERT: A 222 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 256 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8602 (mtt180) REVERT: B 45 ARG cc_start: 0.7942 (ttp80) cc_final: 0.5859 (mmt90) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 0.2274 time to fit residues: 14.3566 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.161304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125687 restraints weight = 3682.633| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.39 r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3228 Z= 0.268 Angle : 0.527 5.354 4375 Z= 0.277 Chirality : 0.042 0.147 444 Planarity : 0.003 0.027 571 Dihedral : 4.172 16.871 429 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.20 % Allowed : 12.35 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.43), residues: 376 helix: 1.25 (0.61), residues: 72 sheet: -0.46 (0.45), residues: 135 loop : -1.15 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.003 0.001 HIS B 84 PHE 0.013 0.002 PHE B 56 TYR 0.012 0.001 TYR A 159 ARG 0.002 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.370 Fit side-chains REVERT: A 72 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7838 (mm-40) REVERT: A 110 LEU cc_start: 0.7899 (tt) cc_final: 0.7472 (tt) REVERT: A 154 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7199 (pt0) REVERT: A 157 ARG cc_start: 0.8048 (ttt-90) cc_final: 0.7762 (ptm-80) REVERT: A 222 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: B 45 ARG cc_start: 0.7932 (ttp80) cc_final: 0.5871 (mmt-90) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2049 time to fit residues: 12.3639 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 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 = 0.3912 r_free = 0.3912 target = 0.162218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127238 restraints weight = 3758.455| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.30 r_work: 0.3316 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3228 Z= 0.249 Angle : 0.515 4.914 4375 Z= 0.271 Chirality : 0.041 0.144 444 Planarity : 0.003 0.026 571 Dihedral : 4.109 16.478 429 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.11 % Allowed : 12.35 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.42), residues: 376 helix: 1.22 (0.61), residues: 73 sheet: -0.38 (0.45), residues: 135 loop : -1.20 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS B 84 PHE 0.012 0.002 PHE B 30 TYR 0.016 0.001 TYR A 159 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.369 Fit side-chains REVERT: A 77 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7644 (t70) REVERT: A 110 LEU cc_start: 0.7926 (tt) cc_final: 0.7514 (tt) REVERT: A 154 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7261 (pt0) REVERT: A 157 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7781 (ptm-80) REVERT: A 222 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 45 ARG cc_start: 0.7972 (ttp80) cc_final: 0.5917 (mmt-90) outliers start: 7 outliers final: 1 residues processed: 50 average time/residue: 0.2035 time to fit residues: 12.1491 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126830 restraints weight = 3644.223| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.40 r_work: 0.3330 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3228 Z= 0.243 Angle : 0.508 4.866 4375 Z= 0.269 Chirality : 0.041 0.141 444 Planarity : 0.003 0.027 571 Dihedral : 4.075 16.551 429 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.81 % Allowed : 12.95 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.42), residues: 376 helix: 1.24 (0.61), residues: 73 sheet: -0.31 (0.45), residues: 135 loop : -1.16 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS C 8 PHE 0.012 0.002 PHE B 30 TYR 0.013 0.001 TYR A 159 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.361 Fit side-chains REVERT: A 77 ASP cc_start: 0.7863 (t0) cc_final: 0.7623 (t70) REVERT: A 110 LEU cc_start: 0.7907 (tt) cc_final: 0.7477 (tt) REVERT: A 154 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7221 (pt0) REVERT: A 157 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7774 (ptm-80) REVERT: A 222 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: B 45 ARG cc_start: 0.7938 (ttp80) cc_final: 0.5856 (mmt-90) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.2112 time to fit residues: 12.3855 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.161615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125670 restraints weight = 3700.913| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.41 r_work: 0.3304 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3228 Z= 0.292 Angle : 0.532 5.452 4375 Z= 0.282 Chirality : 0.042 0.143 444 Planarity : 0.004 0.027 571 Dihedral : 4.220 17.083 429 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.20 % Allowed : 13.86 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.42), residues: 376 helix: 1.22 (0.61), residues: 73 sheet: -0.18 (0.45), residues: 133 loop : -1.23 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS B 84 PHE 0.014 0.002 PHE B 30 TYR 0.016 0.002 TYR A 159 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.342 Fit side-chains REVERT: A 110 LEU cc_start: 0.7952 (tt) cc_final: 0.7482 (tt) REVERT: A 154 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7221 (pt0) REVERT: A 157 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.7776 (ptm-80) REVERT: A 222 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: B 45 ARG cc_start: 0.7990 (ttp80) cc_final: 0.5900 (mmt-90) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.2086 time to fit residues: 12.7575 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.162031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125849 restraints weight = 3750.012| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.42 r_work: 0.3312 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3228 Z= 0.306 Angle : 0.546 5.676 4375 Z= 0.289 Chirality : 0.042 0.143 444 Planarity : 0.004 0.028 571 Dihedral : 4.300 17.322 429 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.51 % Allowed : 14.16 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.43), residues: 376 helix: 1.36 (0.62), residues: 72 sheet: -0.18 (0.45), residues: 133 loop : -1.19 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS B 84 PHE 0.014 0.002 PHE B 30 TYR 0.014 0.002 TYR A 159 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.343 Fit side-chains REVERT: A 77 ASP cc_start: 0.7924 (t0) cc_final: 0.7519 (t70) REVERT: A 110 LEU cc_start: 0.7960 (tt) cc_final: 0.7490 (tt) REVERT: A 154 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7263 (pt0) REVERT: A 157 ARG cc_start: 0.8010 (ttt-90) cc_final: 0.7785 (ptm-80) REVERT: A 222 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 45 ARG cc_start: 0.8011 (ttp80) cc_final: 0.5894 (mmt-90) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.2170 time to fit residues: 12.7876 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.163890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127722 restraints weight = 3653.947| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.40 r_work: 0.3317 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3228 Z= 0.238 Angle : 0.510 5.105 4375 Z= 0.271 Chirality : 0.041 0.140 444 Planarity : 0.003 0.027 571 Dihedral : 4.120 16.591 429 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.20 % Allowed : 14.46 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.43), residues: 376 helix: 1.44 (0.62), residues: 72 sheet: -0.19 (0.45), residues: 135 loop : -1.10 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS C 8 PHE 0.011 0.002 PHE B 30 TYR 0.012 0.001 TYR A 159 ARG 0.004 0.000 ARG A 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.354 Fit side-chains REVERT: A 77 ASP cc_start: 0.7917 (t0) cc_final: 0.7635 (t70) REVERT: A 110 LEU cc_start: 0.7995 (tt) cc_final: 0.7543 (tt) REVERT: A 154 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7247 (pt0) REVERT: A 222 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 45 ARG cc_start: 0.7999 (ttp80) cc_final: 0.5923 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.2339 time to fit residues: 13.5312 Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 19 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.0060 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.1482 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.168514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134191 restraints weight = 3588.661| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.22 r_work: 0.3419 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3228 Z= 0.129 Angle : 0.449 4.122 4375 Z= 0.241 Chirality : 0.040 0.131 444 Planarity : 0.003 0.029 571 Dihedral : 3.618 14.540 429 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.90 % Allowed : 14.76 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.43), residues: 376 helix: 1.64 (0.61), residues: 72 sheet: -0.01 (0.46), residues: 135 loop : -0.94 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE B 70 TYR 0.011 0.001 TYR A 159 ARG 0.004 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.82 seconds wall clock time: 39 minutes 21.98 seconds (2361.98 seconds total)