Starting phenix.real_space_refine on Fri Oct 10 11:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kge_37218/10_2025/8kge_37218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kge_37218/10_2025/8kge_37218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kge_37218/10_2025/8kge_37218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kge_37218/10_2025/8kge_37218.map" model { file = "/net/cci-nas-00/data/ceres_data/8kge_37218/10_2025/8kge_37218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kge_37218/10_2025/8kge_37218.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2238 2.51 5 N 604 2.21 5 O 732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3584 Number of models: 1 Model: "" Number of chains: 2 Chain: "V" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "v" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Time building chain proxies: 1.05, per 1000 atoms: 0.29 Number of scatterers: 3584 At special positions: 0 Unit cell: (93.4554, 106.346, 82.7134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 732 8.00 N 604 7.00 C 2238 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: 0.29 Conformation dependent library (CDL) restraints added in 162.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 880 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 6.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'V' and resid 92 through 103 Processing helix chain 'v' and resid 92 through 103 Processing helix chain 'v' and resid 151 through 156 removed outlier: 3.511A pdb=" N SER v 156 " --> pdb=" O GLU v 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'V' and resid 36 through 38 removed outlier: 5.281A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS V 142 " --> pdb=" O SER V 125 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE V 127 " --> pdb=" O THR V 140 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR V 140 " --> pdb=" O ILE V 127 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS V 129 " --> pdb=" O THR V 138 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR V 138 " --> pdb=" O LYS V 129 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA V 85 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL V 42 " --> pdb=" O ALA V 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 36 through 38 removed outlier: 5.281A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 17.128A pdb=" N ARG V 121 " --> pdb=" O ASP v 56 " (cutoff:3.500A) removed outlier: 14.175A pdb=" N ASP v 56 " --> pdb=" O ARG V 121 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N TRP V 123 " --> pdb=" O SER v 54 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N SER v 54 " --> pdb=" O TRP V 123 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER V 125 " --> pdb=" O ALA v 52 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN v 74 " --> pdb=" O GLU v 53 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR v 55 " --> pdb=" O GLN v 72 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN v 72 " --> pdb=" O TYR v 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 51 through 56 removed outlier: 6.569A pdb=" N THR V 51 " --> pdb=" O LYS V 75 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS V 75 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU V 53 " --> pdb=" O GLY V 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'V' and resid 164 through 166 removed outlier: 3.537A pdb=" N ILE V 214 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 196 through 197 removed outlier: 3.811A pdb=" N GLY V 222 " --> pdb=" O VAL V 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'v' and resid 36 through 38 removed outlier: 5.291A pdb=" N ALA v 107 " --> pdb=" O TYR v 20 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL v 124 " --> pdb=" O THR v 144 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR v 144 " --> pdb=" O VAL v 124 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR v 138 " --> pdb=" O ALA v 130 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA v 85 " --> pdb=" O VAL v 42 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL v 42 " --> pdb=" O ALA v 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'v' and resid 165 through 166 Processing sheet with id=AA8, first strand: chain 'v' and resid 195 through 197 128 hydrogen bonds defined for protein. 342 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: 0.42 Time building geometry restraints manager: 0.42 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: 1178 1.34 - 1.46: 837 1.46 - 1.58: 1619 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3654 Sorted by residual: bond pdb=" CG PRO V 168 " pdb=" CD PRO V 168 " ideal model delta sigma weight residual 1.503 1.404 0.099 3.40e-02 8.65e+02 8.54e+00 bond pdb=" CB GLU V 240 " pdb=" CG GLU V 240 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLU v 102 " pdb=" CG GLU v 102 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" C GLN V 186 " pdb=" N PRO V 187 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 bond pdb=" CA GLU V 188 " pdb=" CB GLU V 188 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 ... (remaining 3649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 4866 2.48 - 4.96: 96 4.96 - 7.44: 18 7.44 - 9.92: 4 9.92 - 12.40: 4 Bond angle restraints: 4988 Sorted by residual: angle pdb=" N PRO V 168 " pdb=" CD PRO V 168 " pdb=" CG PRO V 168 " ideal model delta sigma weight residual 103.20 92.89 10.31 1.50e+00 4.44e-01 4.72e+01 angle pdb=" CA PRO V 168 " pdb=" N PRO V 168 " pdb=" CD PRO V 168 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.77e+01 angle pdb=" CA PRO V 168 " pdb=" CB PRO V 168 " pdb=" CG PRO V 168 " ideal model delta sigma weight residual 104.50 96.47 8.03 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CB MET V 151 " pdb=" CG MET V 151 " pdb=" SD MET V 151 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET v 151 " pdb=" CG MET v 151 " pdb=" SD MET v 151 " ideal model delta sigma weight residual 112.70 124.70 -12.00 3.00e+00 1.11e-01 1.60e+01 ... (remaining 4983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 1764 14.87 - 29.73: 263 29.73 - 44.60: 106 44.60 - 59.46: 21 59.46 - 74.33: 6 Dihedral angle restraints: 2160 sinusoidal: 786 harmonic: 1374 Sorted by residual: dihedral pdb=" CA GLN v 186 " pdb=" C GLN v 186 " pdb=" N PRO v 187 " pdb=" CA PRO v 187 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY V 176 " pdb=" C GLY V 176 " pdb=" N GLN V 177 " pdb=" CA GLN V 177 " ideal model delta harmonic sigma weight residual 180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP V 192 " pdb=" C ASP V 192 " pdb=" N LYS V 193 " pdb=" CA LYS V 193 " ideal model delta harmonic sigma weight residual -180.00 -164.17 -15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 398 0.037 - 0.074: 106 0.074 - 0.111: 66 0.111 - 0.148: 16 0.148 - 0.185: 4 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA ILE V 241 " pdb=" N ILE V 241 " pdb=" C ILE V 241 " pdb=" CB ILE V 241 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR V 162 " pdb=" CA THR V 162 " pdb=" OG1 THR V 162 " pdb=" CG2 THR V 162 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA GLU V 188 " pdb=" N GLU V 188 " pdb=" C GLU V 188 " pdb=" CB GLU V 188 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 587 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN V 186 " 0.047 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO V 187 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO V 187 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO V 187 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE v 226 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO v 227 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO v 227 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO v 227 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE v 226 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE v 226 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE v 226 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO v 227 " -0.013 2.00e-02 2.50e+03 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 104 2.66 - 3.22: 3308 3.22 - 3.78: 5243 3.78 - 4.34: 6751 4.34 - 4.90: 11634 Nonbonded interactions: 27040 Sorted by model distance: nonbonded pdb=" OG1 THR V 180 " pdb=" OG1 THR V 213 " model vdw 2.103 3.040 nonbonded pdb=" OH TYR V 108 " pdb=" OD1 ASN V 145 " model vdw 2.182 3.040 nonbonded pdb=" NE2 GLN V 177 " pdb=" O VAL V 216 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR v 206 " pdb=" OD1 ASN v 217 " model vdw 2.298 3.040 nonbonded pdb=" NZ LYS V 129 " pdb=" OD2 ASP v 118 " model vdw 2.299 3.120 ... (remaining 27035 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 Found NCS groups: ncs_group { reference = chain 'V' selection = chain 'v' } 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 group one per residue 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: 1.620 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 0.099 3654 Z= 0.156 Angle : 0.871 12.404 4988 Z= 0.444 Chirality : 0.048 0.185 590 Planarity : 0.005 0.073 640 Dihedral : 17.206 74.325 1280 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.34 % Favored : 90.46 % Rotamer: Outliers : 10.88 % Allowed : 34.72 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.35), residues: 482 helix: 1.37 (1.06), residues: 24 sheet: -0.83 (0.34), residues: 222 loop : -2.53 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 139 TYR 0.005 0.001 TYR V 55 PHE 0.014 0.002 PHE V 120 TRP 0.003 0.001 TRP V 123 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3654) covalent geometry : angle 0.87089 ( 4988) hydrogen bonds : bond 0.11565 ( 115) hydrogen bonds : angle 6.49065 ( 342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 50 time to evaluate : 0.145 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 37 residues processed: 89 average time/residue: 0.0528 time to fit residues: 6.1156 Evaluate side-chains 84 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 47 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 132 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain V residue 157 THR Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 204 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 125 SER Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 156 SER Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.115272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099406 restraints weight = 8784.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101142 restraints weight = 4480.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102240 restraints weight = 2778.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102855 restraints weight = 1999.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103321 restraints weight = 1635.567| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3654 Z= 0.148 Angle : 0.668 7.410 4988 Z= 0.335 Chirality : 0.048 0.151 590 Planarity : 0.005 0.057 640 Dihedral : 9.131 71.680 567 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.34 % Favored : 90.46 % Rotamer: Outliers : 11.40 % Allowed : 29.27 % Favored : 59.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.35), residues: 482 helix: 1.58 (0.98), residues: 25 sheet: -0.78 (0.34), residues: 224 loop : -2.47 (0.33), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.009 0.001 TYR v 55 PHE 0.014 0.002 PHE V 120 TRP 0.007 0.001 TRP v 18 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3654) covalent geometry : angle 0.66783 ( 4988) hydrogen bonds : bond 0.02958 ( 115) hydrogen bonds : angle 5.41865 ( 342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 51 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: V 90 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: V 111 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8314 (mmm-85) REVERT: V 155 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5795 (mtt-85) REVERT: V 217 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7224 (p0) REVERT: v 72 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7973 (tt0) outliers start: 44 outliers final: 30 residues processed: 89 average time/residue: 0.0700 time to fit residues: 7.7159 Evaluate side-chains 82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 47 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 117 VAL Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 177 GLN Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095484 restraints weight = 8833.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097250 restraints weight = 4420.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098378 restraints weight = 2702.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099012 restraints weight = 1917.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099013 restraints weight = 1545.862| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3654 Z= 0.232 Angle : 0.679 7.437 4988 Z= 0.345 Chirality : 0.049 0.157 590 Planarity : 0.005 0.053 640 Dihedral : 8.762 70.080 546 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 12.69 % Allowed : 28.76 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.35), residues: 482 helix: 1.17 (0.99), residues: 25 sheet: -1.03 (0.34), residues: 220 loop : -2.58 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG v 155 TYR 0.014 0.002 TYR v 55 PHE 0.017 0.002 PHE V 120 TRP 0.011 0.002 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 3654) covalent geometry : angle 0.67944 ( 4988) hydrogen bonds : bond 0.03428 ( 115) hydrogen bonds : angle 5.80251 ( 342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 48 time to evaluate : 0.105 Fit side-chains REVERT: V 90 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: V 111 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8364 (mmm-85) REVERT: V 155 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6065 (mtt-85) REVERT: V 217 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7410 (p0) REVERT: v 72 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: v 87 MET cc_start: 0.4390 (mmt) cc_final: 0.3888 (mmt) REVERT: v 177 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6276 (tp40) outliers start: 49 outliers final: 33 residues processed: 93 average time/residue: 0.0645 time to fit residues: 7.2933 Evaluate side-chains 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 177 GLN Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.114446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098638 restraints weight = 8654.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100443 restraints weight = 4292.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101559 restraints weight = 2605.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102206 restraints weight = 1847.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102675 restraints weight = 1491.816| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3654 Z= 0.132 Angle : 0.620 7.183 4988 Z= 0.314 Chirality : 0.047 0.153 590 Planarity : 0.004 0.053 640 Dihedral : 8.153 67.267 544 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 11.40 % Allowed : 29.79 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.35), residues: 482 helix: 1.59 (1.00), residues: 25 sheet: -0.93 (0.34), residues: 217 loop : -2.53 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.008 0.001 TYR v 55 PHE 0.014 0.002 PHE V 120 TRP 0.007 0.001 TRP v 18 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3654) covalent geometry : angle 0.62034 ( 4988) hydrogen bonds : bond 0.02841 ( 115) hydrogen bonds : angle 5.40477 ( 342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 48 time to evaluate : 0.143 Fit side-chains REVERT: V 90 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: V 111 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8285 (mmm-85) REVERT: V 155 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5893 (mtt-85) REVERT: V 217 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7161 (p0) REVERT: v 63 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: v 72 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7919 (tt0) outliers start: 44 outliers final: 33 residues processed: 87 average time/residue: 0.0609 time to fit residues: 6.5376 Evaluate side-chains 86 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 47 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 72 GLN v 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098352 restraints weight = 8647.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100188 restraints weight = 4234.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101340 restraints weight = 2546.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102054 restraints weight = 1785.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102434 restraints weight = 1418.171| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3654 Z= 0.144 Angle : 0.619 7.093 4988 Z= 0.311 Chirality : 0.047 0.148 590 Planarity : 0.004 0.053 640 Dihedral : 8.022 65.526 543 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 10.10 % Allowed : 30.57 % Favored : 59.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.35), residues: 482 helix: 1.74 (1.00), residues: 25 sheet: -0.66 (0.35), residues: 208 loop : -2.50 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.009 0.001 TYR v 55 PHE 0.018 0.002 PHE V 120 TRP 0.009 0.001 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3654) covalent geometry : angle 0.61863 ( 4988) hydrogen bonds : bond 0.02841 ( 115) hydrogen bonds : angle 5.35884 ( 342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 49 time to evaluate : 0.138 Fit side-chains REVERT: V 90 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: V 111 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8300 (mmm-85) REVERT: V 155 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.5877 (mtt-85) REVERT: V 217 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7178 (p0) REVERT: v 63 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6812 (mp0) outliers start: 39 outliers final: 32 residues processed: 83 average time/residue: 0.0675 time to fit residues: 6.9227 Evaluate side-chains 82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 45 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.114965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098963 restraints weight = 8639.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100903 restraints weight = 4098.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102094 restraints weight = 2425.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102802 restraints weight = 1682.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103100 restraints weight = 1335.964| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3654 Z= 0.126 Angle : 0.624 8.152 4988 Z= 0.310 Chirality : 0.047 0.166 590 Planarity : 0.004 0.053 640 Dihedral : 7.738 63.996 540 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.92 % Favored : 90.87 % Rotamer: Outliers : 11.92 % Allowed : 30.05 % Favored : 58.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.35), residues: 482 helix: 1.87 (1.01), residues: 25 sheet: -0.66 (0.35), residues: 202 loop : -2.45 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.007 0.001 TYR v 55 PHE 0.014 0.002 PHE V 120 TRP 0.008 0.001 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3654) covalent geometry : angle 0.62417 ( 4988) hydrogen bonds : bond 0.02726 ( 115) hydrogen bonds : angle 5.26868 ( 342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 51 time to evaluate : 0.146 Fit side-chains REVERT: V 90 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: V 111 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8291 (mmm-85) REVERT: V 155 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5834 (mtt-85) REVERT: V 217 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7113 (p0) REVERT: v 63 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: v 72 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: v 215 THR cc_start: 0.7785 (m) cc_final: 0.7563 (m) outliers start: 46 outliers final: 36 residues processed: 90 average time/residue: 0.0646 time to fit residues: 7.2174 Evaluate side-chains 91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 49 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.112703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097076 restraints weight = 8846.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098855 restraints weight = 4360.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100001 restraints weight = 2653.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100710 restraints weight = 1880.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101051 restraints weight = 1496.847| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3654 Z= 0.180 Angle : 0.652 8.528 4988 Z= 0.326 Chirality : 0.048 0.168 590 Planarity : 0.004 0.055 640 Dihedral : 7.991 61.363 540 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.13 % Favored : 90.66 % Rotamer: Outliers : 12.18 % Allowed : 29.02 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.35), residues: 482 helix: 1.88 (0.99), residues: 24 sheet: -0.70 (0.35), residues: 204 loop : -2.48 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.011 0.001 TYR v 55 PHE 0.020 0.002 PHE V 120 TRP 0.016 0.001 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3654) covalent geometry : angle 0.65246 ( 4988) hydrogen bonds : bond 0.03051 ( 115) hydrogen bonds : angle 5.53180 ( 342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 48 time to evaluate : 0.128 Fit side-chains REVERT: V 90 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: V 111 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8407 (mmm-85) REVERT: V 155 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.5909 (mtt-85) REVERT: V 217 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7210 (p0) REVERT: v 63 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: v 72 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: v 87 MET cc_start: 0.4075 (mmt) cc_final: 0.3544 (mmt) outliers start: 47 outliers final: 39 residues processed: 89 average time/residue: 0.0671 time to fit residues: 7.3764 Evaluate side-chains 92 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094892 restraints weight = 8886.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096677 restraints weight = 4420.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097820 restraints weight = 2698.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098348 restraints weight = 1904.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098909 restraints weight = 1566.515| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3654 Z= 0.255 Angle : 0.715 9.013 4988 Z= 0.364 Chirality : 0.050 0.178 590 Planarity : 0.005 0.058 640 Dihedral : 8.471 61.104 540 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 12.18 % Allowed : 28.50 % Favored : 59.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.35), residues: 482 helix: 1.09 (1.00), residues: 25 sheet: -0.87 (0.34), residues: 210 loop : -2.58 (0.33), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 155 TYR 0.015 0.002 TYR v 55 PHE 0.022 0.003 PHE V 120 TRP 0.024 0.002 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 3654) covalent geometry : angle 0.71453 ( 4988) hydrogen bonds : bond 0.03521 ( 115) hydrogen bonds : angle 5.93952 ( 342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 47 time to evaluate : 0.153 Fit side-chains REVERT: V 90 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: V 111 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7838 (mtm180) REVERT: V 217 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7269 (p0) REVERT: v 63 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: v 87 MET cc_start: 0.4395 (mmt) cc_final: 0.3879 (mmt) REVERT: v 196 ARG cc_start: 0.8166 (tmm-80) cc_final: 0.7919 (tmm-80) outliers start: 47 outliers final: 39 residues processed: 89 average time/residue: 0.0711 time to fit residues: 7.8455 Evaluate side-chains 89 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 46 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.113300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097587 restraints weight = 8748.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099414 restraints weight = 4278.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100548 restraints weight = 2579.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101287 restraints weight = 1817.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101667 restraints weight = 1438.485| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3654 Z= 0.152 Angle : 0.683 10.529 4988 Z= 0.341 Chirality : 0.048 0.169 590 Planarity : 0.004 0.056 640 Dihedral : 8.157 59.228 540 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 11.14 % Allowed : 30.31 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.35), residues: 482 helix: 1.44 (1.00), residues: 25 sheet: -0.70 (0.35), residues: 201 loop : -2.54 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.008 0.001 TYR v 55 PHE 0.019 0.002 PHE V 120 TRP 0.014 0.001 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3654) covalent geometry : angle 0.68254 ( 4988) hydrogen bonds : bond 0.02987 ( 115) hydrogen bonds : angle 5.62516 ( 342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 48 time to evaluate : 0.170 Fit side-chains REVERT: V 90 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: V 111 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8325 (mmm-85) REVERT: V 217 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7172 (p0) REVERT: v 63 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: v 72 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: v 196 ARG cc_start: 0.8035 (tmm-80) cc_final: 0.7781 (tmm-80) REVERT: v 215 THR cc_start: 0.7696 (m) cc_final: 0.7493 (m) outliers start: 43 outliers final: 37 residues processed: 85 average time/residue: 0.0623 time to fit residues: 6.6454 Evaluate side-chains 90 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 48 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain V residue 178 SER Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 213 THR Chi-restraints excluded: chain V residue 214 ILE Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 217 ASN Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 96 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 193 LYS Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.116112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100470 restraints weight = 8756.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102214 restraints weight = 4412.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103369 restraints weight = 2716.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104057 restraints weight = 1931.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104341 restraints weight = 1546.926| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3654 Z= 0.119 Angle : 0.645 10.916 4988 Z= 0.318 Chirality : 0.047 0.159 590 Planarity : 0.004 0.056 640 Dihedral : 7.705 55.565 540 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 10.88 % Allowed : 30.31 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.35), residues: 482 helix: 2.30 (1.01), residues: 24 sheet: -0.81 (0.35), residues: 209 loop : -2.33 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.007 0.001 TYR v 55 PHE 0.015 0.002 PHE V 120 TRP 0.008 0.001 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3654) covalent geometry : angle 0.64503 ( 4988) hydrogen bonds : bond 0.02641 ( 115) hydrogen bonds : angle 5.23373 ( 342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 52 time to evaluate : 0.142 Fit side-chains REVERT: V 90 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: V 111 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8246 (mmm-85) REVERT: V 155 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5729 (mtt-85) REVERT: V 206 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7356 (p) REVERT: v 63 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: v 72 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: v 196 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7646 (tmm-80) outliers start: 42 outliers final: 30 residues processed: 86 average time/residue: 0.0652 time to fit residues: 6.9669 Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 121 ARG Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain V residue 232 ASN Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 51 THR Chi-restraints excluded: chain v residue 63 GLU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 72 GLN Chi-restraints excluded: chain v residue 83 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 131 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 162 THR Chi-restraints excluded: chain v residue 174 VAL Chi-restraints excluded: chain v residue 180 THR Chi-restraints excluded: chain v residue 181 LEU Chi-restraints excluded: chain v residue 183 VAL Chi-restraints excluded: chain v residue 201 ASP Chi-restraints excluded: chain v residue 216 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097223 restraints weight = 8618.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099035 restraints weight = 4295.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100164 restraints weight = 2614.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100901 restraints weight = 1845.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101278 restraints weight = 1471.171| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3654 Z= 0.187 Angle : 0.697 10.983 4988 Z= 0.347 Chirality : 0.048 0.162 590 Planarity : 0.004 0.057 640 Dihedral : 7.084 51.820 533 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 9.07 % Allowed : 31.09 % Favored : 59.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.35), residues: 482 helix: 1.96 (1.00), residues: 24 sheet: -0.61 (0.36), residues: 203 loop : -2.43 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 155 TYR 0.010 0.001 TYR v 55 PHE 0.020 0.002 PHE V 120 TRP 0.018 0.001 TRP v 123 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 3654) covalent geometry : angle 0.69666 ( 4988) hydrogen bonds : bond 0.03092 ( 115) hydrogen bonds : angle 5.50585 ( 342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 765.59 seconds wall clock time: 13 minutes 57.96 seconds (837.96 seconds total)