Starting phenix.real_space_refine on Wed Jul 1 23:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hbw_34645/07_2026/8hbw_34645.cif" } resolution = 2.57 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= 0.003 sd= 0.159 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 18 5.16 5 C 2109 2.51 5 N 548 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2179 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'ATP': 1, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 0.99, per 1000 atoms: 0.30 Number of scatterers: 3309 At special positions: 0 Unit cell: (65.052, 71.724, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 7 15.00 O 627 8.00 N 548 7.00 C 2109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 120.0 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 62.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 76 through 94 removed outlier: 4.367A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.629A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 4.224A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.609A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.892A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 627 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: 0.47 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 547 1.32 - 1.44: 902 1.44 - 1.56: 1893 1.56 - 1.68: 13 1.68 - 1.81: 27 Bond restraints: 3382 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.454 -0.112 1.50e-02 4.44e+03 5.57e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.43e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.10e+01 ... (remaining 3377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 4506 3.41 - 6.82: 70 6.82 - 10.22: 14 10.22 - 13.63: 1 13.63 - 17.04: 1 Bond angle restraints: 4592 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 119.46 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.51 -7.47 1.15e+00 7.59e-01 4.24e+01 ... (remaining 4587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1767 17.12 - 34.24: 142 34.24 - 51.36: 42 51.36 - 68.49: 7 68.49 - 85.61: 5 Dihedral angle restraints: 1963 sinusoidal: 780 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N ASP A 210 " pdb=" CA ASP A 210 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU A 100 " pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " pdb=" OE1 GLU A 100 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 1960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 331 0.043 - 0.086: 138 0.086 - 0.129: 33 0.129 - 0.172: 5 0.172 - 0.214: 3 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA LYS A 66 " pdb=" N LYS A 66 " pdb=" C LYS A 66 " pdb=" CB LYS A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 261 " pdb=" N GLU A 261 " pdb=" C GLU A 261 " pdb=" CB GLU A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ARG A 238 " pdb=" N ARG A 238 " pdb=" C ARG A 238 " pdb=" CB ARG A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 507 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 10 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 84 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C GLN A 84 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 84 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 85 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 101 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 101 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 360 2.74 - 3.28: 3189 3.28 - 3.82: 5979 3.82 - 4.36: 7174 4.36 - 4.90: 12102 Nonbonded interactions: 28804 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O THR A 108 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 247 " model vdw 2.266 3.040 nonbonded pdb=" O LYS A 292 " pdb=" OG SER A 296 " model vdw 2.276 3.040 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.320 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.323 3.040 ... (remaining 28799 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.850 Find NCS groups from input model: 0.010 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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 : 0.010 0.124 3383 Z= 0.619 Angle : 1.055 17.042 4594 Z= 0.645 Chirality : 0.050 0.214 510 Planarity : 0.005 0.057 567 Dihedral : 14.544 85.607 1206 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.60 (0.39), residues: 410 helix: 1.83 (0.32), residues: 221 sheet: -0.32 (0.61), residues: 60 loop : 0.59 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG B 104 TYR 0.014 0.002 TYR A 157 PHE 0.018 0.003 PHE A 223 TRP 0.007 0.002 TRP A 173 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.62 ( 3382) covalent geometry : angle 1.05315 / 0.64 ( 4592) SS BOND : bond 0.00499 / 0.26 ( 1) SS BOND : angle 3.02118 / 1.75 ( 2) hydrogen bonds : bond 0.10650 / 7.55 ( 227) hydrogen bonds : angle 6.85175 / 5.10 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.124 Fit side-chains REVERT: A 55 LYS cc_start: 0.8108 (tttp) cc_final: 0.7810 (tptp) REVERT: A 161 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6715 (mtt90) REVERT: A 206 ILE cc_start: 0.6885 (mm) cc_final: 0.6564 (mp) REVERT: A 248 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8426 (ptmt) REVERT: A 293 ARG cc_start: 0.6520 (ptm-80) cc_final: 0.6132 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.6498 time to fit residues: 41.2607 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119948 restraints weight = 3605.253| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 0.89 r_work: 0.3225 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3383 Z= 0.143 Angle : 0.535 6.816 4594 Z= 0.282 Chirality : 0.040 0.138 510 Planarity : 0.005 0.051 567 Dihedral : 10.037 76.455 500 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 9.20 % Favored : 89.32 % 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: 2.46 (0.40), residues: 410 helix: 2.66 (0.32), residues: 221 sheet: 0.06 (0.65), residues: 54 loop : 0.67 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.008 0.001 TYR A 74 PHE 0.009 0.002 PHE A 223 TRP 0.007 0.001 TRP B 111 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3382) covalent geometry : angle 0.53410 / 0.28 ( 4592) SS BOND : bond 0.00237 / 0.12 ( 1) SS BOND : angle 1.59329 / 0.94 ( 2) hydrogen bonds : bond 0.03920 / 2.70 ( 227) hydrogen bonds : angle 5.59330 / 4.19 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.078 Fit side-chains REVERT: A 55 LYS cc_start: 0.8311 (tttp) cc_final: 0.7829 (tptp) REVERT: A 117 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 161 ARG cc_start: 0.7959 (ttt180) cc_final: 0.6637 (mtt90) REVERT: A 206 ILE cc_start: 0.6783 (mm) cc_final: 0.6411 (mp) REVERT: A 293 ARG cc_start: 0.6410 (ptm-80) cc_final: 0.6018 (tmt-80) outliers start: 5 outliers final: 0 residues processed: 63 average time/residue: 0.6210 time to fit residues: 40.1407 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117491 restraints weight = 3630.618| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.95 r_work: 0.3186 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3383 Z= 0.162 Angle : 0.545 7.213 4594 Z= 0.283 Chirality : 0.041 0.138 510 Planarity : 0.005 0.047 567 Dihedral : 9.774 75.420 500 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 11.28 % Favored : 86.05 % 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: 2.63 (0.40), residues: 410 helix: 2.89 (0.32), residues: 221 sheet: 0.01 (0.65), residues: 54 loop : 0.61 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.010 0.001 TYR A 157 PHE 0.012 0.002 PHE A 223 TRP 0.005 0.001 TRP B 57 HIS 0.002 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 3382) covalent geometry : angle 0.54410 / 0.28 ( 4592) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 1.65910 / 0.96 ( 2) hydrogen bonds : bond 0.03940 / 2.68 ( 227) hydrogen bonds : angle 5.57572 / 4.19 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.139 Fit side-chains REVERT: A 55 LYS cc_start: 0.8354 (tttp) cc_final: 0.7848 (tptp) REVERT: A 57 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8180 (t) REVERT: A 117 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 161 ARG cc_start: 0.8013 (ttt180) cc_final: 0.6632 (mtt90) REVERT: A 206 ILE cc_start: 0.6797 (mm) cc_final: 0.6437 (mp) REVERT: A 293 ARG cc_start: 0.6454 (ptm-80) cc_final: 0.6080 (tmt-80) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.6013 time to fit residues: 37.0424 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118562 restraints weight = 3629.635| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.94 r_work: 0.3200 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3383 Z= 0.148 Angle : 0.534 7.870 4594 Z= 0.275 Chirality : 0.040 0.139 510 Planarity : 0.005 0.043 567 Dihedral : 9.679 75.614 500 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.26 % Allowed : 11.87 % Favored : 84.87 % 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: 2.73 (0.40), residues: 410 helix: 2.94 (0.32), residues: 221 sheet: 0.09 (0.65), residues: 54 loop : 0.69 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.009 0.001 TYR A 157 PHE 0.011 0.002 PHE A 223 TRP 0.005 0.001 TRP A 280 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3382) covalent geometry : angle 0.53327 / 0.27 ( 4592) SS BOND : bond 0.00215 / 0.11 ( 1) SS BOND : angle 1.49734 / 0.87 ( 2) hydrogen bonds : bond 0.03782 / 2.57 ( 227) hydrogen bonds : angle 5.47363 / 4.11 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.126 Fit side-chains REVERT: A 53 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7425 (tpt-90) REVERT: A 55 LYS cc_start: 0.8354 (tttp) cc_final: 0.7858 (tptp) REVERT: A 57 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8179 (t) REVERT: A 70 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6516 (mtp-110) REVERT: A 117 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7630 (tt) REVERT: A 161 ARG cc_start: 0.8011 (ttt180) cc_final: 0.6624 (mtt90) REVERT: A 206 ILE cc_start: 0.6719 (mm) cc_final: 0.6382 (mp) REVERT: A 293 ARG cc_start: 0.6480 (ptm-80) cc_final: 0.6108 (tmt-80) outliers start: 11 outliers final: 5 residues processed: 59 average time/residue: 0.6161 time to fit residues: 37.3471 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118268 restraints weight = 3596.433| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.90 r_work: 0.3198 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3383 Z= 0.166 Angle : 0.550 8.095 4594 Z= 0.283 Chirality : 0.041 0.135 510 Planarity : 0.005 0.041 567 Dihedral : 9.636 74.120 500 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.56 % Allowed : 12.46 % Favored : 83.98 % 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: 2.71 (0.40), residues: 410 helix: 2.93 (0.32), residues: 221 sheet: -0.00 (0.65), residues: 54 loop : 0.74 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.010 0.001 TYR A 157 PHE 0.013 0.002 PHE A 223 TRP 0.005 0.001 TRP A 280 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 3382) covalent geometry : angle 0.54949 / 0.28 ( 4592) SS BOND : bond 0.00238 / 0.13 ( 1) SS BOND : angle 1.64440 / 0.96 ( 2) hydrogen bonds : bond 0.03897 / 2.64 ( 227) hydrogen bonds : angle 5.48782 / 4.12 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.141 Fit side-chains REVERT: A 53 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7294 (tpt-90) REVERT: A 55 LYS cc_start: 0.8378 (tttp) cc_final: 0.7890 (tptp) REVERT: A 57 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 70 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6615 (mtp-110) REVERT: A 117 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 161 ARG cc_start: 0.8040 (ttt180) cc_final: 0.6687 (mtt90) REVERT: A 206 ILE cc_start: 0.6748 (mm) cc_final: 0.6413 (mp) REVERT: A 293 ARG cc_start: 0.6517 (ptm-80) cc_final: 0.6147 (tmt-80) outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.5973 time to fit residues: 36.8094 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119965 restraints weight = 3582.656| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.91 r_work: 0.3215 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3383 Z= 0.139 Angle : 0.527 8.370 4594 Z= 0.270 Chirality : 0.040 0.128 510 Planarity : 0.004 0.039 567 Dihedral : 9.350 73.488 500 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.26 % Allowed : 13.65 % Favored : 83.09 % 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: 2.79 (0.40), residues: 410 helix: 3.00 (0.32), residues: 221 sheet: 0.02 (0.65), residues: 54 loop : 0.74 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.008 0.001 TYR A 157 PHE 0.010 0.001 PHE A 223 TRP 0.006 0.001 TRP A 280 HIS 0.001 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3382) covalent geometry : angle 0.52647 / 0.27 ( 4592) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 1.34508 / 0.79 ( 2) hydrogen bonds : bond 0.03686 / 2.49 ( 227) hydrogen bonds : angle 5.36898 / 4.04 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.129 Fit side-chains REVERT: A 53 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7439 (tpt-90) REVERT: A 55 LYS cc_start: 0.8365 (tttp) cc_final: 0.7883 (tptp) REVERT: A 57 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8197 (t) REVERT: A 70 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6498 (mtp-110) REVERT: A 117 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 161 ARG cc_start: 0.8024 (ttt180) cc_final: 0.6679 (mtt90) REVERT: A 206 ILE cc_start: 0.6659 (mm) cc_final: 0.6336 (mp) REVERT: A 293 ARG cc_start: 0.6475 (ptm-80) cc_final: 0.6111 (tmt-80) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.5977 time to fit residues: 37.4581 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122710 restraints weight = 3605.186| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.90 r_work: 0.3231 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3383 Z= 0.117 Angle : 0.507 8.520 4594 Z= 0.259 Chirality : 0.039 0.125 510 Planarity : 0.004 0.039 567 Dihedral : 9.134 73.568 500 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.26 % Allowed : 13.95 % Favored : 82.79 % 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: 2.95 (0.40), residues: 410 helix: 3.12 (0.32), residues: 221 sheet: 0.21 (0.67), residues: 54 loop : 0.79 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.007 0.001 TYR A 157 PHE 0.011 0.001 PHE B 101 TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 3382) covalent geometry : angle 0.50656 / 0.26 ( 4592) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 1.07769 / 0.63 ( 2) hydrogen bonds : bond 0.03455 / 2.34 ( 227) hydrogen bonds : angle 5.20950 / 3.92 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.133 Fit side-chains REVERT: A 53 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7476 (tpt-90) REVERT: A 55 LYS cc_start: 0.8312 (tttp) cc_final: 0.7847 (tptp) REVERT: A 57 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8177 (t) REVERT: A 70 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6633 (mtp-110) REVERT: A 117 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 161 ARG cc_start: 0.8021 (ttt180) cc_final: 0.6673 (mtt90) REVERT: A 206 ILE cc_start: 0.6494 (mm) cc_final: 0.6169 (mp) REVERT: A 293 ARG cc_start: 0.6443 (ptm-80) cc_final: 0.6107 (tmt-80) outliers start: 11 outliers final: 4 residues processed: 67 average time/residue: 0.5982 time to fit residues: 41.1492 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119744 restraints weight = 3639.203| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.09 r_work: 0.3199 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3383 Z= 0.129 Angle : 0.528 8.612 4594 Z= 0.270 Chirality : 0.039 0.126 510 Planarity : 0.005 0.038 567 Dihedral : 9.066 73.303 500 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % Favored : 81.90 % 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: 2.97 (0.40), residues: 410 helix: 3.10 (0.32), residues: 222 sheet: 0.30 (0.68), residues: 54 loop : 0.81 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.008 0.001 TYR A 157 PHE 0.012 0.002 PHE B 101 TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3382) covalent geometry : angle 0.52677 / 0.27 ( 4592) SS BOND : bond 0.00150 / 0.08 ( 1) SS BOND : angle 1.59003 / 0.93 ( 2) hydrogen bonds : bond 0.03568 / 2.40 ( 227) hydrogen bonds : angle 5.20493 / 3.92 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.139 Fit side-chains REVERT: A 53 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7513 (tmt170) REVERT: A 55 LYS cc_start: 0.8319 (tttp) cc_final: 0.7808 (tptp) REVERT: A 57 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8166 (t) REVERT: A 70 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6606 (mtp-110) REVERT: A 117 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7624 (tt) REVERT: A 161 ARG cc_start: 0.8045 (ttt180) cc_final: 0.6594 (mtt90) REVERT: A 206 ILE cc_start: 0.6451 (mm) cc_final: 0.6120 (mp) REVERT: A 293 ARG cc_start: 0.6415 (ptm-80) cc_final: 0.6053 (tmt-80) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.6292 time to fit residues: 39.4123 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119041 restraints weight = 3601.833| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.97 r_work: 0.3196 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3383 Z= 0.145 Angle : 0.540 8.593 4594 Z= 0.276 Chirality : 0.040 0.130 510 Planarity : 0.004 0.037 567 Dihedral : 9.083 72.032 500 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % Favored : 81.90 % 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: 2.91 (0.40), residues: 410 helix: 3.07 (0.32), residues: 222 sheet: 0.18 (0.68), residues: 54 loop : 0.80 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.009 0.001 TYR A 157 PHE 0.011 0.002 PHE A 223 TRP 0.005 0.001 TRP B 57 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 3382) covalent geometry : angle 0.53866 / 0.28 ( 4592) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 1.67710 / 0.98 ( 2) hydrogen bonds : bond 0.03723 / 2.50 ( 227) hydrogen bonds : angle 5.28049 / 3.98 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.131 Fit side-chains REVERT: A 53 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7212 (tpt-90) REVERT: A 55 LYS cc_start: 0.8288 (tttp) cc_final: 0.7755 (tptp) REVERT: A 57 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8117 (t) REVERT: A 70 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6491 (mtp-110) REVERT: A 117 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7525 (tt) REVERT: A 161 ARG cc_start: 0.7959 (ttt180) cc_final: 0.6480 (mtt90) REVERT: A 206 ILE cc_start: 0.6495 (mm) cc_final: 0.6149 (mp) REVERT: A 293 ARG cc_start: 0.6318 (ptm-80) cc_final: 0.5949 (tmt-80) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.6172 time to fit residues: 37.9801 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120262 restraints weight = 3773.981| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.08 r_work: 0.3243 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3383 Z= 0.145 Angle : 0.541 8.695 4594 Z= 0.276 Chirality : 0.040 0.131 510 Planarity : 0.004 0.037 567 Dihedral : 9.053 71.309 500 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.67 % Allowed : 15.73 % Favored : 81.60 % 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: 2.87 (0.40), residues: 410 helix: 3.05 (0.32), residues: 222 sheet: 0.09 (0.67), residues: 54 loop : 0.79 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.009 0.001 TYR A 157 PHE 0.011 0.002 PHE A 223 TRP 0.005 0.001 TRP A 280 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 3382) covalent geometry : angle 0.53957 / 0.28 ( 4592) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 1.68649 / 0.98 ( 2) hydrogen bonds : bond 0.03714 / 2.49 ( 227) hydrogen bonds : angle 5.28000 / 3.97 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.130 Fit side-chains REVERT: A 53 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7503 (tpt-90) REVERT: A 55 LYS cc_start: 0.8384 (tttp) cc_final: 0.7906 (tptp) REVERT: A 57 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8181 (t) REVERT: A 70 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6605 (mtp-110) REVERT: A 117 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 161 ARG cc_start: 0.8049 (ttt180) cc_final: 0.6693 (mtt90) REVERT: A 206 ILE cc_start: 0.6600 (mm) cc_final: 0.6260 (mp) REVERT: A 293 ARG cc_start: 0.6487 (ptm-80) cc_final: 0.6116 (tmt-80) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.6352 time to fit residues: 38.4635 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120152 restraints weight = 3852.400| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.09 r_work: 0.3228 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3383 Z= 0.152 Angle : 0.546 8.642 4594 Z= 0.279 Chirality : 0.041 0.131 510 Planarity : 0.004 0.037 567 Dihedral : 9.060 71.237 500 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.97 % Allowed : 15.13 % Favored : 81.90 % 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: 2.85 (0.40), residues: 410 helix: 3.03 (0.32), residues: 222 sheet: 0.09 (0.68), residues: 54 loop : 0.78 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.009 0.001 TYR A 157 PHE 0.011 0.002 PHE A 223 TRP 0.005 0.001 TRP A 280 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 3382) covalent geometry : angle 0.54442 / 0.28 ( 4592) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 1.75243 / 1.02 ( 2) hydrogen bonds : bond 0.03766 / 2.53 ( 227) hydrogen bonds : angle 5.29973 / 3.99 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.82 seconds wall clock time: 27 minutes 27.84 seconds (1647.84 seconds total)