Starting phenix.real_space_refine on Wed Jun 3 10:09:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3l_65604/06_2026/9w3l_65604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3l_65604/06_2026/9w3l_65604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3l_65604/06_2026/9w3l_65604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3l_65604/06_2026/9w3l_65604.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3l_65604/06_2026/9w3l_65604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3l_65604/06_2026/9w3l_65604.cif" } resolution = 2.76 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1972 2.51 5 N 507 2.21 5 O 526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3021 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2054 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 3, 'PHE:plan': 3, 'ARG:plan': 2, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 967 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 0.94, per 1000 atoms: 0.31 Number of scatterers: 3021 At special positions: 0 Unit cell: (84.24, 122.4, 54.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 526 8.00 N 507 7.00 C 1972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.04 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: 0.25 Conformation dependent library (CDL) restraints added in 125.0 milliseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 4 sheets defined 56.1% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.696A pdb=" N VAL A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 108 through 139 removed outlier: 5.503A pdb=" N ASP A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TRP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 removed outlier: 3.500A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 removed outlier: 4.186A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 175' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 211 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.800A pdb=" N PHE A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 263 removed outlier: 3.598A pdb=" N ARG A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.600A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 297 through 310 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.752A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.532A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.363A pdb=" N GLY B 11 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 50 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG B 39 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU B 48 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 100 182 hydrogen bonds defined for protein. 528 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: 0.38 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 941 1.34 - 1.46: 791 1.46 - 1.58: 1339 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 3095 Sorted by residual: bond pdb=" CA THR B 102 " pdb=" CB THR B 102 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.99e-01 bond pdb=" CB PRO A 283 " pdb=" CG PRO A 283 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.69e-01 bond pdb=" C LEU A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.58e-01 bond pdb=" CB ARG B 101 " pdb=" CG ARG B 101 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.29e-01 bond pdb=" C TYR A 206 " pdb=" N PRO A 207 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.25e-01 ... (remaining 3090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 4123 1.54 - 3.08: 80 3.08 - 4.62: 16 4.62 - 6.16: 3 6.16 - 7.70: 3 Bond angle restraints: 4225 Sorted by residual: angle pdb=" C PHE A 90 " pdb=" N SER A 91 " pdb=" CA SER A 91 " ideal model delta sigma weight residual 122.15 115.52 6.63 2.83e+00 1.25e-01 5.49e+00 angle pdb=" C ARG B 101 " pdb=" N THR B 102 " pdb=" CA THR B 102 " ideal model delta sigma weight residual 121.54 125.77 -4.23 1.91e+00 2.74e-01 4.90e+00 angle pdb=" CA LEU B 19 " pdb=" CB LEU B 19 " pdb=" CG LEU B 19 " ideal model delta sigma weight residual 116.30 124.00 -7.70 3.50e+00 8.16e-02 4.84e+00 angle pdb=" CA LEU A 188 " pdb=" CB LEU A 188 " pdb=" CG LEU A 188 " ideal model delta sigma weight residual 116.30 123.20 -6.90 3.50e+00 8.16e-02 3.89e+00 angle pdb=" N ILE A 129 " pdb=" CA ILE A 129 " pdb=" C ILE A 129 " ideal model delta sigma weight residual 110.62 112.60 -1.98 1.02e+00 9.61e-01 3.77e+00 ... (remaining 4220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 1596 14.94 - 29.87: 142 29.87 - 44.80: 41 44.80 - 59.74: 6 59.74 - 74.67: 3 Dihedral angle restraints: 1788 sinusoidal: 631 harmonic: 1157 Sorted by residual: dihedral pdb=" CA LYS A 112 " pdb=" C LYS A 112 " pdb=" N SER A 113 " pdb=" CA SER A 113 " ideal model delta harmonic sigma weight residual 180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TRP A 272 " pdb=" C TRP A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CG LYS A 318 " pdb=" CD LYS A 318 " pdb=" CE LYS A 318 " pdb=" NZ LYS A 318 " ideal model delta sinusoidal sigma weight residual 180.00 123.18 56.82 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 269 0.026 - 0.053: 149 0.053 - 0.079: 47 0.079 - 0.106: 24 0.106 - 0.132: 11 Chirality restraints: 500 Sorted by residual: chirality pdb=" CB THR B 28 " pdb=" CA THR B 28 " pdb=" OG1 THR B 28 " pdb=" CG2 THR B 28 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA LEU A 168 " pdb=" N LEU A 168 " pdb=" C LEU A 168 " pdb=" CB LEU A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CB THR B 91 " pdb=" CA THR B 91 " pdb=" OG1 THR B 91 " pdb=" CG2 THR B 91 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 497 not shown) Planarity restraints: 517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 168 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO A 169 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 250 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ARG A 250 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A 250 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 251 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 249 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C THR A 249 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 249 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 250 " 0.010 2.00e-02 2.50e+03 ... (remaining 514 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.07: 1982 3.07 - 3.53: 3095 3.53 - 3.99: 4260 3.99 - 4.44: 4971 4.44 - 4.90: 7852 Nonbonded interactions: 22160 Sorted by model distance: nonbonded pdb=" O PHE A 90 " pdb=" CA SER A 91 " model vdw 2.616 2.776 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.618 3.040 nonbonded pdb=" O PHE A 220 " pdb=" OG1 THR A 223 " model vdw 2.619 3.040 nonbonded pdb=" N ASP B 34 " pdb=" OD1 ASP B 34 " model vdw 2.635 3.120 nonbonded pdb=" N SER B 71 " pdb=" O SER B 71 " model vdw 2.644 2.496 ... (remaining 22155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.770 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.003 0.038 3097 Z= 0.146 Angle : 0.577 7.698 4229 Z= 0.295 Chirality : 0.041 0.132 500 Planarity : 0.006 0.057 517 Dihedral : 13.133 74.674 1034 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: -0.21 (0.43), residues: 391 helix: 0.41 (0.37), residues: 202 sheet: 1.04 (0.61), residues: 75 loop : -1.89 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.011 0.001 TYR A 221 PHE 0.016 0.001 PHE A 216 TRP 0.023 0.001 TRP A 272 HIS 0.002 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 3095) covalent geometry : angle 0.57613 / 0.29 ( 4225) SS BOND : bond 0.00573 / 0.27 ( 2) SS BOND : angle 0.89364 / 0.55 ( 4) hydrogen bonds : bond 0.15747 / 12.07 ( 182) hydrogen bonds : angle 6.79826 / 5.30 ( 528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.088 Fit side-chains REVERT: A 78 LEU cc_start: 0.8213 (tt) cc_final: 0.7972 (tm) REVERT: A 202 PHE cc_start: 0.7773 (t80) cc_final: 0.7481 (t80) REVERT: A 295 MET cc_start: 0.8628 (tmm) cc_final: 0.8382 (tmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1801 time to fit residues: 13.5327 Evaluate side-chains 62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118963 restraints weight = 4638.521| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.42 r_work: 0.3628 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3097 Z= 0.198 Angle : 0.676 9.203 4229 Z= 0.323 Chirality : 0.043 0.145 500 Planarity : 0.005 0.048 517 Dihedral : 3.813 16.610 427 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.94 % Allowed : 12.09 % Favored : 84.97 % 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 are not related in a simple way. whole: 0.72 (0.43), residues: 391 helix: 1.44 (0.37), residues: 205 sheet: 1.24 (0.61), residues: 74 loop : -1.92 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 101 TYR 0.012 0.002 TYR A 222 PHE 0.031 0.002 PHE A 216 TRP 0.024 0.002 TRP A 272 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 3095) covalent geometry : angle 0.67588 / 0.32 ( 4225) SS BOND : bond 0.00775 / 0.37 ( 2) SS BOND : angle 0.75593 / 0.43 ( 4) hydrogen bonds : bond 0.06157 / 4.12 ( 182) hydrogen bonds : angle 4.36474 / 3.27 ( 528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.096 Fit side-chains REVERT: A 48 LEU cc_start: 0.8328 (mt) cc_final: 0.8101 (mt) REVERT: A 78 LEU cc_start: 0.8251 (tt) cc_final: 0.7997 (tm) REVERT: A 295 MET cc_start: 0.8718 (tmm) cc_final: 0.8415 (tmm) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.1989 time to fit residues: 14.4738 Evaluate side-chains 71 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.141463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.121262 restraints weight = 4631.079| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.38 r_work: 0.3658 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3097 Z= 0.138 Angle : 0.596 7.322 4229 Z= 0.284 Chirality : 0.041 0.124 500 Planarity : 0.005 0.054 517 Dihedral : 3.582 16.684 427 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.27 % Allowed : 15.03 % Favored : 81.70 % 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 are not related in a simple way. whole: 1.12 (0.43), residues: 391 helix: 1.96 (0.37), residues: 202 sheet: 1.26 (0.61), residues: 74 loop : -1.96 (0.53), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.006 0.001 TYR B 80 PHE 0.029 0.002 PHE A 216 TRP 0.016 0.001 TRP A 272 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3095) covalent geometry : angle 0.59594 / 0.28 ( 4225) SS BOND : bond 0.00534 / 0.25 ( 2) SS BOND : angle 0.66161 / 0.41 ( 4) hydrogen bonds : bond 0.05127 / 3.40 ( 182) hydrogen bonds : angle 3.85290 / 2.86 ( 528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.095 Fit side-chains REVERT: A 48 LEU cc_start: 0.8312 (mt) cc_final: 0.8085 (mt) REVERT: A 78 LEU cc_start: 0.8183 (tt) cc_final: 0.7922 (tm) REVERT: A 295 MET cc_start: 0.8659 (tmm) cc_final: 0.8364 (tmm) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.1924 time to fit residues: 14.1358 Evaluate side-chains 63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116787 restraints weight = 4629.696| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.38 r_work: 0.3597 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3097 Z= 0.235 Angle : 0.678 8.606 4229 Z= 0.330 Chirality : 0.043 0.134 500 Planarity : 0.005 0.057 517 Dihedral : 3.916 16.890 427 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.23 % Allowed : 15.69 % Favored : 79.08 % 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 are not related in a simple way. whole: 0.97 (0.43), residues: 391 helix: 1.87 (0.37), residues: 202 sheet: 1.20 (0.60), residues: 74 loop : -2.09 (0.51), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 101 TYR 0.012 0.002 TYR B 80 PHE 0.026 0.002 PHE A 202 TRP 0.017 0.002 TRP A 270 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 3095) covalent geometry : angle 0.67739 / 0.33 ( 4225) SS BOND : bond 0.00932 / 0.44 ( 2) SS BOND : angle 0.80369 / 0.39 ( 4) hydrogen bonds : bond 0.06607 / 4.34 ( 182) hydrogen bonds : angle 4.15945 / 3.09 ( 528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.114 Fit side-chains REVERT: A 48 LEU cc_start: 0.8399 (mt) cc_final: 0.8166 (mt) REVERT: A 78 LEU cc_start: 0.8282 (tt) cc_final: 0.8012 (tm) REVERT: A 295 MET cc_start: 0.8738 (tmm) cc_final: 0.8430 (tmm) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.1925 time to fit residues: 14.6205 Evaluate side-chains 75 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117165 restraints weight = 4680.646| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.41 r_work: 0.3610 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3097 Z= 0.193 Angle : 0.650 9.169 4229 Z= 0.315 Chirality : 0.043 0.182 500 Planarity : 0.005 0.060 517 Dihedral : 3.912 16.805 427 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.23 % Allowed : 18.30 % Favored : 76.47 % 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 are not related in a simple way. whole: 1.01 (0.43), residues: 391 helix: 1.94 (0.37), residues: 202 sheet: 1.28 (0.61), residues: 74 loop : -2.20 (0.48), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.008 0.001 TYR B 100 PHE 0.028 0.002 PHE A 202 TRP 0.013 0.001 TRP A 270 HIS 0.002 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 3095) covalent geometry : angle 0.64981 / 0.31 ( 4225) SS BOND : bond 0.00721 / 0.34 ( 2) SS BOND : angle 0.66403 / 0.39 ( 4) hydrogen bonds : bond 0.06056 / 3.96 ( 182) hydrogen bonds : angle 4.05574 / 3.00 ( 528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.108 Fit side-chains REVERT: A 48 LEU cc_start: 0.8395 (mt) cc_final: 0.8159 (mt) REVERT: A 78 LEU cc_start: 0.8258 (tt) cc_final: 0.7983 (tm) REVERT: A 295 MET cc_start: 0.8702 (tmm) cc_final: 0.8459 (tmm) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.2201 time to fit residues: 17.0172 Evaluate side-chains 77 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.139075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118359 restraints weight = 4684.476| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.41 r_work: 0.3623 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3097 Z= 0.155 Angle : 0.610 9.255 4229 Z= 0.295 Chirality : 0.042 0.154 500 Planarity : 0.006 0.062 517 Dihedral : 3.793 16.556 427 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.90 % Allowed : 18.30 % Favored : 76.80 % 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 are not related in a simple way. whole: 1.19 (0.43), residues: 391 helix: 2.05 (0.37), residues: 205 sheet: 1.24 (0.61), residues: 74 loop : -2.05 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 228 TYR 0.005 0.001 TYR B 80 PHE 0.028 0.002 PHE A 202 TRP 0.009 0.001 TRP A 270 HIS 0.003 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 3095) covalent geometry : angle 0.60942 / 0.30 ( 4225) SS BOND : bond 0.00608 / 0.29 ( 2) SS BOND : angle 0.69719 / 0.44 ( 4) hydrogen bonds : bond 0.05377 / 3.50 ( 182) hydrogen bonds : angle 3.84233 / 2.84 ( 528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.119 Fit side-chains REVERT: A 48 LEU cc_start: 0.8370 (mt) cc_final: 0.8142 (mt) REVERT: A 55 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 78 LEU cc_start: 0.8181 (tt) cc_final: 0.7900 (tm) REVERT: A 295 MET cc_start: 0.8670 (tmm) cc_final: 0.8402 (tmm) outliers start: 15 outliers final: 9 residues processed: 72 average time/residue: 0.2305 time to fit residues: 17.6352 Evaluate side-chains 76 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 37 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.139574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118591 restraints weight = 4729.577| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.45 r_work: 0.3634 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3097 Z= 0.142 Angle : 0.586 7.247 4229 Z= 0.287 Chirality : 0.042 0.175 500 Planarity : 0.005 0.066 517 Dihedral : 3.717 16.141 427 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.92 % Allowed : 19.28 % Favored : 76.80 % 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 are not related in a simple way. whole: 1.17 (0.43), residues: 391 helix: 1.99 (0.37), residues: 206 sheet: 1.25 (0.61), residues: 74 loop : -2.03 (0.50), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.005 0.001 TYR B 80 PHE 0.028 0.002 PHE A 202 TRP 0.008 0.001 TRP A 270 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3095) covalent geometry : angle 0.58593 / 0.29 ( 4225) SS BOND : bond 0.00541 / 0.26 ( 2) SS BOND : angle 0.68130 / 0.44 ( 4) hydrogen bonds : bond 0.05138 / 3.35 ( 182) hydrogen bonds : angle 3.73081 / 2.74 ( 528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.083 Fit side-chains REVERT: A 48 LEU cc_start: 0.8387 (mt) cc_final: 0.8156 (mt) REVERT: A 78 LEU cc_start: 0.8173 (tt) cc_final: 0.7876 (tm) REVERT: A 295 MET cc_start: 0.8615 (tmm) cc_final: 0.8361 (tmm) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.2051 time to fit residues: 14.3761 Evaluate side-chains 70 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120039 restraints weight = 4771.095| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.42 r_work: 0.3633 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3097 Z= 0.159 Angle : 0.650 9.315 4229 Z= 0.304 Chirality : 0.043 0.159 500 Planarity : 0.005 0.061 517 Dihedral : 3.769 16.323 427 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.27 % Allowed : 20.59 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.43), residues: 391 helix: 1.90 (0.37), residues: 205 sheet: 1.24 (0.61), residues: 74 loop : -2.00 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.009 0.001 TYR B 80 PHE 0.028 0.001 PHE A 202 TRP 0.009 0.001 TRP A 270 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 3095) covalent geometry : angle 0.65044 / 0.30 ( 4225) SS BOND : bond 0.00666 / 0.32 ( 2) SS BOND : angle 0.69983 / 0.42 ( 4) hydrogen bonds : bond 0.05420 / 3.51 ( 182) hydrogen bonds : angle 3.78975 / 2.77 ( 528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.116 Fit side-chains REVERT: A 48 LEU cc_start: 0.8351 (mt) cc_final: 0.8150 (mt) REVERT: A 78 LEU cc_start: 0.8127 (tt) cc_final: 0.7844 (tm) REVERT: A 122 MET cc_start: 0.8104 (tpp) cc_final: 0.7880 (mmt) REVERT: A 295 MET cc_start: 0.8566 (tmm) cc_final: 0.8300 (tmm) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.2067 time to fit residues: 14.6089 Evaluate side-chains 72 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.2816 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119583 restraints weight = 4692.292| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.43 r_work: 0.3658 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3097 Z= 0.131 Angle : 0.599 7.455 4229 Z= 0.284 Chirality : 0.041 0.142 500 Planarity : 0.005 0.072 517 Dihedral : 3.659 15.897 427 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.92 % Allowed : 20.26 % Favored : 75.82 % 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 are not related in a simple way. whole: 1.07 (0.43), residues: 391 helix: 1.97 (0.37), residues: 205 sheet: 0.79 (0.57), residues: 84 loop : -2.06 (0.53), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 101 TYR 0.008 0.001 TYR B 80 PHE 0.029 0.001 PHE A 202 TRP 0.008 0.001 TRP A 116 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3095) covalent geometry : angle 0.59848 / 0.28 ( 4225) SS BOND : bond 0.00487 / 0.23 ( 2) SS BOND : angle 0.90353 / 0.59 ( 4) hydrogen bonds : bond 0.04767 / 3.08 ( 182) hydrogen bonds : angle 3.65682 / 2.67 ( 528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.107 Fit side-chains REVERT: A 48 LEU cc_start: 0.8432 (mt) cc_final: 0.8204 (mt) REVERT: A 78 LEU cc_start: 0.8110 (tt) cc_final: 0.7810 (tm) REVERT: A 295 MET cc_start: 0.8543 (tmm) cc_final: 0.8246 (tmm) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.2161 time to fit residues: 15.1877 Evaluate side-chains 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 2 optimal weight: 0.4980 chunk 35 optimal weight: 0.0670 chunk 28 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.140792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.119755 restraints weight = 4667.670| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.42 r_work: 0.3662 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3097 Z= 0.125 Angle : 0.585 8.033 4229 Z= 0.279 Chirality : 0.041 0.125 500 Planarity : 0.005 0.072 517 Dihedral : 3.596 15.842 427 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.29 % Allowed : 21.57 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.43), residues: 391 helix: 2.08 (0.36), residues: 204 sheet: 1.28 (0.60), residues: 74 loop : -1.90 (0.51), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.009 0.001 TYR B 80 PHE 0.029 0.002 PHE A 202 TRP 0.008 0.001 TRP A 116 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3095) covalent geometry : angle 0.58476 / 0.28 ( 4225) SS BOND : bond 0.00467 / 0.22 ( 2) SS BOND : angle 0.76633 / 0.50 ( 4) hydrogen bonds : bond 0.04603 / 3.00 ( 182) hydrogen bonds : angle 3.62706 / 2.63 ( 528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.115 Fit side-chains REVERT: A 48 LEU cc_start: 0.8357 (mt) cc_final: 0.8146 (mt) REVERT: A 78 LEU cc_start: 0.8065 (tt) cc_final: 0.7767 (tm) REVERT: A 264 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 295 MET cc_start: 0.8479 (tmm) cc_final: 0.8080 (tmm) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 0.2100 time to fit residues: 14.9926 Evaluate side-chains 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 14 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.140234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119421 restraints weight = 4627.790| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.39 r_work: 0.3637 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3097 Z= 0.155 Angle : 0.649 9.581 4229 Z= 0.301 Chirality : 0.042 0.135 500 Planarity : 0.005 0.070 517 Dihedral : 3.700 15.869 427 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.29 % Allowed : 22.55 % Favored : 75.16 % 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 are not related in a simple way. whole: 1.25 (0.43), residues: 391 helix: 2.03 (0.36), residues: 204 sheet: 1.38 (0.60), residues: 73 loop : -1.90 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.012 0.001 TYR B 80 PHE 0.029 0.002 PHE A 202 TRP 0.010 0.001 TRP A 270 HIS 0.002 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 3095) covalent geometry : angle 0.64846 / 0.30 ( 4225) SS BOND : bond 0.00653 / 0.31 ( 2) SS BOND : angle 0.71287 / 0.42 ( 4) hydrogen bonds : bond 0.05250 / 3.39 ( 182) hydrogen bonds : angle 3.73461 / 2.72 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1181.32 seconds wall clock time: 20 minutes 57.03 seconds (1257.03 seconds total)