Starting phenix.real_space_refine on Wed Mar 5 17:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xdc_22136/03_2025/6xdc_22136.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xdc_22136/03_2025/6xdc_22136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2025/6xdc_22136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2025/6xdc_22136.map" model { file = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2025/6xdc_22136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2025/6xdc_22136.cif" } resolution = 2.9 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= 0.101 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 16 5.16 5 C 2094 2.51 5 N 490 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 3150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.83 Number of scatterers: 3150 At special positions: 0 Unit cell: (55.713, 62.535, 94.371, 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 16 16.00 O 550 8.00 N 490 7.00 C 2094 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: 0.65 Conformation dependent library (CDL) restraints added in 345.1 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 50.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.806A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 Processing helix chain 'A' and resid 102 through 134 removed outlier: 3.618A pdb=" N LEU A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.881A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.067A pdb=" N THR A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.825A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 Processing helix chain 'B' and resid 102 through 133 removed outlier: 3.716A pdb=" N LEU B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.831A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.074A pdb=" N THR B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 removed outlier: 5.422A pdb=" N LEU A 214 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 216 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 172 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 183 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 160 removed outlier: 5.387A pdb=" N LEU B 214 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 216 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 172 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP B 183 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 585 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: 0.83 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 912 1.34 - 1.46: 719 1.46 - 1.57: 1595 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3244 Sorted by residual: bond pdb=" CB GLN A 185 " pdb=" CG GLN A 185 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.09e+00 bond pdb=" CB GLN B 185 " pdb=" CG GLN B 185 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" C ALA A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 2.05e+00 bond pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.96e+00 ... (remaining 3239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 4249 1.72 - 3.44: 148 3.44 - 5.17: 20 5.17 - 6.89: 4 6.89 - 8.61: 3 Bond angle restraints: 4424 Sorted by residual: angle pdb=" CA TYR A 107 " pdb=" CB TYR A 107 " pdb=" CG TYR A 107 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.19e+01 angle pdb=" CA TYR B 107 " pdb=" CB TYR B 107 " pdb=" CG TYR B 107 " ideal model delta sigma weight residual 113.90 120.05 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" N ASN A 137 " pdb=" CA ASN A 137 " pdb=" C ASN A 137 " ideal model delta sigma weight residual 109.81 117.09 -7.28 2.21e+00 2.05e-01 1.08e+01 angle pdb=" N ASN B 137 " pdb=" CA ASN B 137 " pdb=" C ASN B 137 " ideal model delta sigma weight residual 109.81 117.00 -7.19 2.21e+00 2.05e-01 1.06e+01 angle pdb=" OG1 THR A 170 " pdb=" CB THR A 170 " pdb=" CG2 THR A 170 " ideal model delta sigma weight residual 109.30 102.79 6.51 2.00e+00 2.50e-01 1.06e+01 ... (remaining 4419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 1544 12.27 - 24.53: 191 24.53 - 36.80: 67 36.80 - 49.07: 18 49.07 - 61.34: 10 Dihedral angle restraints: 1830 sinusoidal: 684 harmonic: 1146 Sorted by residual: dihedral pdb=" CA LEU B 140 " pdb=" C LEU B 140 " pdb=" N TYR B 141 " pdb=" CA TYR B 141 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU A 140 " pdb=" C LEU A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual 180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR B 189 " pdb=" C TYR B 189 " pdb=" N THR B 190 " pdb=" CA THR B 190 " ideal model delta harmonic sigma weight residual -180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 407 0.071 - 0.141: 83 0.141 - 0.212: 8 0.212 - 0.282: 3 0.282 - 0.353: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" CB ILE B 236 " pdb=" CA ILE B 236 " pdb=" CG1 ILE B 236 " pdb=" CG2 ILE B 236 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL A 197 " pdb=" CA VAL A 197 " pdb=" CG1 VAL A 197 " pdb=" CG2 VAL A 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 499 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 137 " -0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO B 138 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 137 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO A 138 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 103 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO B 104 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.034 5.00e-02 4.00e+02 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 831 2.80 - 3.33: 2598 3.33 - 3.85: 5072 3.85 - 4.38: 5521 4.38 - 4.90: 9971 Nonbonded interactions: 23993 Sorted by model distance: nonbonded pdb=" OG1 THR B 151 " pdb=" O TYR B 154 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.284 3.040 nonbonded pdb=" O PHE B 114 " pdb=" OG SER B 117 " model vdw 2.375 3.040 nonbonded pdb=" O PHE A 114 " pdb=" OG SER A 117 " model vdw 2.378 3.040 nonbonded pdb=" N ASP A 238 " pdb=" OD1 ASP A 238 " model vdw 2.381 3.120 ... (remaining 23988 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.090 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 0.065 3244 Z= 0.365 Angle : 0.788 8.610 4424 Z= 0.444 Chirality : 0.062 0.353 502 Planarity : 0.008 0.079 528 Dihedral : 13.654 61.336 1098 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.15 % Allowed : 15.23 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.34), residues: 378 helix: -1.09 (0.30), residues: 168 sheet: -1.40 (0.42), residues: 106 loop : -3.07 (0.45), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 149 HIS 0.007 0.002 HIS B 182 PHE 0.010 0.001 PHE B 43 TYR 0.020 0.002 TYR A 107 ARG 0.002 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.315 Fit side-chains REVERT: A 61 LYS cc_start: 0.8333 (mttp) cc_final: 0.8072 (mttt) REVERT: A 134 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7708 (mtp180) REVERT: A 192 LYS cc_start: 0.8574 (tttt) cc_final: 0.8114 (tttp) REVERT: A 215 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: B 61 LYS cc_start: 0.8331 (mttp) cc_final: 0.8046 (mttt) REVERT: B 113 TYR cc_start: 0.8092 (m-10) cc_final: 0.7876 (m-80) REVERT: B 134 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7740 (mtp180) REVERT: B 192 LYS cc_start: 0.8621 (tttt) cc_final: 0.8153 (tttp) REVERT: B 215 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6921 (m-10) outliers start: 4 outliers final: 1 residues processed: 66 average time/residue: 0.6193 time to fit residues: 43.0036 Evaluate side-chains 47 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 215 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 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 204 HIS B 93 HIS B 185 GLN B 204 HIS B 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.166109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137587 restraints weight = 4060.746| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.90 r_work: 0.3642 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3244 Z= 0.222 Angle : 0.576 9.187 4424 Z= 0.319 Chirality : 0.045 0.144 502 Planarity : 0.006 0.063 528 Dihedral : 6.421 57.674 428 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.45 % Allowed : 16.67 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.40), residues: 378 helix: 1.39 (0.38), residues: 168 sheet: -0.80 (0.47), residues: 96 loop : -2.73 (0.45), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.003 0.001 HIS A 182 PHE 0.007 0.001 PHE A 43 TYR 0.022 0.002 TYR B 107 ARG 0.002 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.283 Fit side-chains REVERT: A 61 LYS cc_start: 0.8052 (mttp) cc_final: 0.7837 (mttt) REVERT: A 66 LYS cc_start: 0.7484 (mttt) cc_final: 0.7238 (mttm) REVERT: A 134 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7196 (mtp180) REVERT: A 192 LYS cc_start: 0.8350 (tttt) cc_final: 0.7870 (tttp) REVERT: B 66 LYS cc_start: 0.7478 (mttt) cc_final: 0.7227 (mttm) REVERT: B 134 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7260 (tpt170) REVERT: B 192 LYS cc_start: 0.8317 (tttt) cc_final: 0.7823 (tttp) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.7228 time to fit residues: 44.6561 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.167372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139147 restraints weight = 3987.516| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.85 r_work: 0.3655 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3244 Z= 0.185 Angle : 0.544 9.243 4424 Z= 0.300 Chirality : 0.043 0.137 502 Planarity : 0.005 0.057 528 Dihedral : 6.136 56.709 426 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.45 % Allowed : 17.53 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.43), residues: 378 helix: 2.20 (0.40), residues: 170 sheet: -0.79 (0.48), residues: 96 loop : -2.60 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.003 0.001 HIS B 182 PHE 0.017 0.001 PHE A 207 TYR 0.027 0.002 TYR B 107 ARG 0.000 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.366 Fit side-chains REVERT: A 134 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7190 (tpt170) REVERT: A 154 TYR cc_start: 0.7410 (t80) cc_final: 0.7118 (t80) REVERT: A 192 LYS cc_start: 0.8391 (tttt) cc_final: 0.7892 (tttp) REVERT: A 194 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7862 (mm-30) REVERT: A 215 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: B 134 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7236 (mmt180) REVERT: B 154 TYR cc_start: 0.7444 (t80) cc_final: 0.7209 (t80) REVERT: B 162 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 192 LYS cc_start: 0.8238 (tttt) cc_final: 0.7761 (ttmp) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.8280 time to fit residues: 54.4495 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 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 = 0.4022 r_free = 0.4022 target = 0.165873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137501 restraints weight = 4095.266| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.87 r_work: 0.3626 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3244 Z= 0.210 Angle : 0.575 10.473 4424 Z= 0.311 Chirality : 0.044 0.137 502 Planarity : 0.005 0.056 528 Dihedral : 6.125 57.450 426 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.31 % Allowed : 19.83 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.43), residues: 378 helix: 2.55 (0.40), residues: 170 sheet: -0.83 (0.49), residues: 96 loop : -2.47 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 193 HIS 0.003 0.001 HIS A 182 PHE 0.021 0.001 PHE A 207 TYR 0.027 0.002 TYR A 107 ARG 0.000 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.337 Fit side-chains REVERT: A 127 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7252 (mm) REVERT: A 134 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7185 (tpt170) REVERT: A 192 LYS cc_start: 0.8294 (tttt) cc_final: 0.7756 (ttmp) REVERT: A 194 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7737 (mm-30) REVERT: B 134 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7280 (mmt-90) REVERT: B 162 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 192 LYS cc_start: 0.8237 (tttt) cc_final: 0.7837 (mttp) outliers start: 15 outliers final: 11 residues processed: 48 average time/residue: 0.8264 time to fit residues: 41.4406 Evaluate side-chains 48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.0020 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.168753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140434 restraints weight = 4066.892| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.91 r_work: 0.3662 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3244 Z= 0.160 Angle : 0.536 9.338 4424 Z= 0.291 Chirality : 0.042 0.134 502 Planarity : 0.005 0.055 528 Dihedral : 5.883 56.433 426 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.02 % Allowed : 21.55 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.44), residues: 378 helix: 2.74 (0.40), residues: 170 sheet: -0.80 (0.50), residues: 96 loop : -2.34 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 193 HIS 0.003 0.001 HIS B 182 PHE 0.018 0.001 PHE B 207 TYR 0.026 0.001 TYR A 107 ARG 0.000 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.318 Fit side-chains REVERT: A 134 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7153 (tpt170) REVERT: A 162 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8229 (p) REVERT: A 192 LYS cc_start: 0.8268 (tttt) cc_final: 0.7752 (tttp) REVERT: A 194 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 215 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: B 134 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7259 (mmt180) REVERT: B 162 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8270 (p) REVERT: B 192 LYS cc_start: 0.8270 (tttt) cc_final: 0.7868 (mttp) outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 0.8422 time to fit residues: 44.7394 Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.166411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138117 restraints weight = 4234.845| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.93 r_work: 0.3622 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3244 Z= 0.216 Angle : 0.566 8.813 4424 Z= 0.309 Chirality : 0.044 0.136 502 Planarity : 0.005 0.055 528 Dihedral : 6.056 57.186 426 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.74 % Allowed : 21.84 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.44), residues: 378 helix: 2.75 (0.40), residues: 170 sheet: -0.86 (0.50), residues: 96 loop : -2.33 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 193 HIS 0.004 0.001 HIS B 182 PHE 0.021 0.001 PHE A 207 TYR 0.027 0.002 TYR A 107 ARG 0.000 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.331 Fit side-chains REVERT: A 127 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7275 (mm) REVERT: A 134 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7186 (mmt180) REVERT: A 162 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8217 (p) REVERT: A 192 LYS cc_start: 0.8314 (tttt) cc_final: 0.7795 (ttmp) REVERT: A 194 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7836 (mm-30) REVERT: B 134 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7223 (mtp180) REVERT: B 162 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 192 LYS cc_start: 0.8289 (tttt) cc_final: 0.7804 (ttmp) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.8543 time to fit residues: 41.8226 Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137469 restraints weight = 4122.863| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.88 r_work: 0.3624 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3244 Z= 0.233 Angle : 0.573 8.634 4424 Z= 0.314 Chirality : 0.044 0.135 502 Planarity : 0.005 0.055 528 Dihedral : 6.126 57.203 426 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.74 % Allowed : 21.84 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.44), residues: 378 helix: 2.75 (0.40), residues: 170 sheet: -0.88 (0.50), residues: 96 loop : -2.23 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 193 HIS 0.004 0.001 HIS B 182 PHE 0.023 0.001 PHE A 207 TYR 0.026 0.002 TYR A 107 ARG 0.001 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.275 Fit side-chains REVERT: A 127 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7253 (mm) REVERT: A 134 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7224 (tpt170) REVERT: A 162 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8224 (p) REVERT: A 192 LYS cc_start: 0.8324 (tttt) cc_final: 0.7796 (ttmp) REVERT: A 194 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7865 (mm-30) REVERT: B 134 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7248 (mtp180) REVERT: B 162 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 192 LYS cc_start: 0.8323 (tttt) cc_final: 0.7827 (ttmp) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 0.8331 time to fit residues: 42.5103 Evaluate side-chains 48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.164728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136254 restraints weight = 4177.379| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.92 r_work: 0.3614 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3244 Z= 0.236 Angle : 0.581 8.459 4424 Z= 0.319 Chirality : 0.044 0.134 502 Planarity : 0.005 0.056 528 Dihedral : 6.159 57.157 426 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.89 % Allowed : 20.98 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.44), residues: 378 helix: 2.79 (0.39), residues: 170 sheet: -0.91 (0.50), residues: 96 loop : -2.23 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 193 HIS 0.004 0.001 HIS B 182 PHE 0.026 0.001 PHE A 207 TYR 0.026 0.002 TYR A 107 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.367 Fit side-chains REVERT: A 127 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 134 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7205 (tpt170) REVERT: A 192 LYS cc_start: 0.8284 (tttt) cc_final: 0.7752 (ttmp) REVERT: A 194 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 134 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7207 (mtp180) REVERT: B 162 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 192 LYS cc_start: 0.8274 (tttt) cc_final: 0.7756 (tttp) outliers start: 17 outliers final: 9 residues processed: 51 average time/residue: 0.9121 time to fit residues: 48.4125 Evaluate side-chains 44 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.0030 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.167767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138652 restraints weight = 4144.736| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.95 r_work: 0.3637 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3244 Z= 0.182 Angle : 0.583 12.412 4424 Z= 0.312 Chirality : 0.043 0.139 502 Planarity : 0.005 0.055 528 Dihedral : 5.968 56.016 426 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.02 % Allowed : 22.70 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.44), residues: 378 helix: 2.82 (0.39), residues: 170 sheet: -0.87 (0.51), residues: 96 loop : -2.16 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 193 HIS 0.003 0.001 HIS B 182 PHE 0.013 0.001 PHE B 207 TYR 0.025 0.001 TYR A 107 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.344 Fit side-chains REVERT: A 127 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7302 (mm) REVERT: A 134 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7207 (mmt-90) REVERT: A 162 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 192 LYS cc_start: 0.8247 (tttt) cc_final: 0.7704 (tttp) REVERT: A 194 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 215 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: B 134 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7191 (mtp180) REVERT: B 162 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.8027 (p) REVERT: B 192 LYS cc_start: 0.8373 (tttt) cc_final: 0.7853 (tttp) REVERT: B 194 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 215 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7007 (m-10) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.8478 time to fit residues: 40.7004 Evaluate side-chains 43 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.166487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137616 restraints weight = 4071.569| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.90 r_work: 0.3629 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3244 Z= 0.204 Angle : 0.600 11.873 4424 Z= 0.322 Chirality : 0.044 0.140 502 Planarity : 0.005 0.056 528 Dihedral : 6.015 56.439 426 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.45 % Allowed : 23.56 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.44), residues: 378 helix: 2.86 (0.39), residues: 170 sheet: -0.86 (0.51), residues: 96 loop : -2.14 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 193 HIS 0.003 0.001 HIS B 182 PHE 0.024 0.001 PHE A 207 TYR 0.026 0.001 TYR A 107 ARG 0.000 0.000 ARG B 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.347 Fit side-chains REVERT: A 127 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7286 (mm) REVERT: A 134 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7216 (mmt-90) REVERT: A 162 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 192 LYS cc_start: 0.8277 (tttt) cc_final: 0.7693 (tttp) REVERT: A 194 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 198 LYS cc_start: 0.6182 (mptp) cc_final: 0.5978 (mmtp) REVERT: B 134 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7198 (mtp180) REVERT: B 162 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 192 LYS cc_start: 0.8372 (tttt) cc_final: 0.7843 (tttp) REVERT: B 194 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7866 (mt-10) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.8559 time to fit residues: 38.4499 Evaluate side-chains 44 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.169203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140444 restraints weight = 4134.119| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.99 r_work: 0.3676 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3244 Z= 0.163 Angle : 0.575 11.691 4424 Z= 0.308 Chirality : 0.042 0.137 502 Planarity : 0.005 0.055 528 Dihedral : 5.814 55.323 426 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.02 % Allowed : 22.99 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.44), residues: 378 helix: 2.93 (0.39), residues: 170 sheet: -0.76 (0.52), residues: 96 loop : -2.12 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 193 HIS 0.002 0.001 HIS B 182 PHE 0.027 0.001 PHE A 207 TYR 0.024 0.001 TYR A 107 ARG 0.001 0.000 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.61 seconds wall clock time: 38 minutes 34.70 seconds (2314.70 seconds total)