Starting phenix.real_space_refine on Tue Feb 3 15:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hiw_52204/02_2026/9hiw_52204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hiw_52204/02_2026/9hiw_52204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hiw_52204/02_2026/9hiw_52204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hiw_52204/02_2026/9hiw_52204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hiw_52204/02_2026/9hiw_52204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hiw_52204/02_2026/9hiw_52204.map" } resolution = 3.1 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= 0.005 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 19 5.16 5 C 2877 2.51 5 N 738 2.21 5 O 791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4425 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2062 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2293 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 19, 'TRANS': 265} Chain breaks: 3 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Time building chain proxies: 1.15, per 1000 atoms: 0.26 Number of scatterers: 4425 At special positions: 0 Unit cell: (77.18, 85.125, 69.235, 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 19 16.00 O 791 8.00 N 738 7.00 C 2877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 208.3 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 56.4% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.953A pdb=" N VAL A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 Processing helix chain 'A' and resid 228 through 246 Processing helix chain 'A' and resid 252 through 269 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 287 through 303 Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.565A pdb=" N PHE A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 343 removed outlier: 3.576A pdb=" N LEU A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.886A pdb=" N TYR A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 414 through 419 removed outlier: 6.009A pdb=" N LYS A 417 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 121 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 145 through 149 removed outlier: 4.432A pdb=" N LEU B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.174A pdb=" N ASP B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.578A pdb=" N VAL B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 287 removed outlier: 6.079A pdb=" N PHE B 285 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 11 removed outlier: 6.867A pdb=" N LYS B 20 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS B 9 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL B 18 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 11 removed outlier: 6.867A pdb=" N LYS B 20 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS B 9 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL B 18 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 68 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU B 81 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B 66 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86 217 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: 0.70 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1388 1.34 - 1.46: 958 1.46 - 1.58: 2153 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 4531 Sorted by residual: bond pdb=" CB VAL B 230 " pdb=" CG2 VAL B 230 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.79e-01 bond pdb=" CB MET B 1 " pdb=" CG MET B 1 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.62e-01 bond pdb=" N PRO B 204 " pdb=" CA PRO B 204 " ideal model delta sigma weight residual 1.479 1.467 0.012 1.56e-02 4.11e+03 6.25e-01 bond pdb=" C PRO B 253 " pdb=" N PRO B 254 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.19e-02 7.06e+03 5.46e-01 bond pdb=" CB ASN A 415 " pdb=" CG ASN A 415 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.18e-01 ... (remaining 4526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 6068 1.93 - 3.85: 66 3.85 - 5.78: 4 5.78 - 7.70: 1 7.70 - 9.63: 1 Bond angle restraints: 6140 Sorted by residual: angle pdb=" CB MET B 1 " pdb=" CG MET B 1 " pdb=" SD MET B 1 " ideal model delta sigma weight residual 112.70 122.33 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C HIS B 125 " pdb=" N ARG B 126 " pdb=" CA ARG B 126 " ideal model delta sigma weight residual 121.54 125.31 -3.77 1.91e+00 2.74e-01 3.89e+00 angle pdb=" CA MET B 1 " pdb=" CB MET B 1 " pdb=" CG MET B 1 " ideal model delta sigma weight residual 114.10 117.96 -3.86 2.00e+00 2.50e-01 3.73e+00 angle pdb=" N PRO B 253 " pdb=" CA PRO B 253 " pdb=" C PRO B 253 " ideal model delta sigma weight residual 110.70 113.00 -2.30 1.22e+00 6.72e-01 3.56e+00 angle pdb=" N HIS B 121 " pdb=" CA HIS B 121 " pdb=" C HIS B 121 " ideal model delta sigma weight residual 110.35 107.76 2.59 1.38e+00 5.25e-01 3.52e+00 ... (remaining 6135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 2348 17.66 - 35.32: 295 35.32 - 52.98: 79 52.98 - 70.65: 14 70.65 - 88.31: 6 Dihedral angle restraints: 2742 sinusoidal: 1126 harmonic: 1616 Sorted by residual: dihedral pdb=" CG ARG B 260 " pdb=" CD ARG B 260 " pdb=" NE ARG B 260 " pdb=" CZ ARG B 260 " ideal model delta sinusoidal sigma weight residual -90.00 -134.82 44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " pdb=" CD GLU A 223 " pdb=" OE1 GLU A 223 " ideal model delta sinusoidal sigma weight residual 0.00 87.38 -87.38 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP B 68 " pdb=" CB ASP B 68 " pdb=" CG ASP B 68 " pdb=" OD1 ASP B 68 " ideal model delta sinusoidal sigma weight residual -30.00 -84.44 54.44 1 2.00e+01 2.50e-03 1.00e+01 ... (remaining 2739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 477 0.032 - 0.064: 149 0.064 - 0.096: 51 0.096 - 0.127: 13 0.127 - 0.159: 5 Chirality restraints: 695 Sorted by residual: chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE B 135 " pdb=" N ILE B 135 " pdb=" C ILE B 135 " pdb=" CB ILE B 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 63 " pdb=" N ILE B 63 " pdb=" C ILE B 63 " pdb=" CB ILE B 63 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 692 not shown) Planarity restraints: 770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 345 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 346 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 60 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 61 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 252 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 253 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " 0.018 5.00e-02 4.00e+02 ... (remaining 767 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 467 2.75 - 3.28: 4320 3.28 - 3.82: 7741 3.82 - 4.36: 9452 4.36 - 4.90: 16035 Nonbonded interactions: 38015 Sorted by model distance: nonbonded pdb=" OH TYR A 238 " pdb=" O LEU A 306 " model vdw 2.207 3.040 nonbonded pdb=" O ALA A 307 " pdb=" NH2 ARG B 122 " model vdw 2.231 3.120 nonbonded pdb=" OH TYR A 347 " pdb=" OG1 THR A 397 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" N LEU B 166 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR B 72 " pdb=" O LYS B 75 " model vdw 2.258 3.040 ... (remaining 38010 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.860 Find NCS groups from input model: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 0.029 4531 Z= 0.119 Angle : 0.496 9.630 6140 Z= 0.252 Chirality : 0.038 0.159 695 Planarity : 0.004 0.035 770 Dihedral : 16.941 88.307 1694 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.05 % Allowed : 21.72 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.36), residues: 536 helix: 1.95 (0.32), residues: 271 sheet: -1.02 (0.93), residues: 26 loop : -0.32 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 199 TYR 0.010 0.001 TYR A 347 PHE 0.011 0.001 PHE B 152 TRP 0.009 0.001 TRP A 372 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4531) covalent geometry : angle 0.49580 ( 6140) hydrogen bonds : bond 0.12163 ( 210) hydrogen bonds : angle 5.58975 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.182 Fit side-chains REVERT: A 407 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8111 (mm-40) REVERT: B 12 GLU cc_start: 0.6823 (tp30) cc_final: 0.6199 (tp30) REVERT: B 34 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8286 (ptpt) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.0910 time to fit residues: 10.0373 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.122467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.103091 restraints weight = 5106.277| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.53 r_work: 0.2879 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4531 Z= 0.123 Angle : 0.487 6.931 6140 Z= 0.247 Chirality : 0.039 0.153 695 Planarity : 0.004 0.038 770 Dihedral : 5.288 49.534 604 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.05 % Allowed : 20.70 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.21 (0.36), residues: 536 helix: 2.04 (0.32), residues: 274 sheet: -1.61 (0.82), residues: 26 loop : -0.37 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 199 TYR 0.009 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.010 0.001 TRP A 372 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4531) covalent geometry : angle 0.48733 ( 6140) hydrogen bonds : bond 0.03683 ( 210) hydrogen bonds : angle 4.56233 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.183 Fit side-chains REVERT: A 224 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 378 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7912 (mpt180) REVERT: B 12 GLU cc_start: 0.6936 (tp30) cc_final: 0.6303 (tp30) REVERT: B 34 LYS cc_start: 0.8724 (ptmm) cc_final: 0.8186 (ptpt) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.0961 time to fit residues: 11.1552 Evaluate side-chains 90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 0.0030 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.104715 restraints weight = 4998.965| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.50 r_work: 0.2900 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4531 Z= 0.109 Angle : 0.473 7.200 6140 Z= 0.236 Chirality : 0.038 0.152 695 Planarity : 0.004 0.040 770 Dihedral : 4.399 27.656 597 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.46 % Allowed : 19.88 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.28 (0.36), residues: 536 helix: 2.12 (0.32), residues: 274 sheet: -1.69 (0.80), residues: 26 loop : -0.36 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.009 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.009 0.001 TRP A 372 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4531) covalent geometry : angle 0.47299 ( 6140) hydrogen bonds : bond 0.03270 ( 210) hydrogen bonds : angle 4.38454 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.189 Fit side-chains REVERT: A 224 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 277 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 378 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7899 (mpt180) REVERT: B 12 GLU cc_start: 0.6947 (tp30) cc_final: 0.6321 (tp30) REVERT: B 34 LYS cc_start: 0.8652 (ptmm) cc_final: 0.8098 (ptpt) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.0900 time to fit residues: 10.8082 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.124714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105277 restraints weight = 4988.313| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.52 r_work: 0.2903 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4531 Z= 0.104 Angle : 0.465 6.342 6140 Z= 0.232 Chirality : 0.038 0.151 695 Planarity : 0.004 0.040 770 Dihedral : 4.367 27.973 597 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.46 % Allowed : 19.67 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.33 (0.37), residues: 536 helix: 2.15 (0.32), residues: 276 sheet: -1.75 (0.79), residues: 26 loop : -0.32 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.009 0.001 TYR A 199 PHE 0.010 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4531) covalent geometry : angle 0.46521 ( 6140) hydrogen bonds : bond 0.03083 ( 210) hydrogen bonds : angle 4.26775 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.181 Fit side-chains REVERT: A 277 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 378 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7905 (mpt180) REVERT: B 12 GLU cc_start: 0.6895 (tp30) cc_final: 0.6260 (tp30) REVERT: B 34 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8110 (ptpt) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.0982 time to fit residues: 11.6356 Evaluate side-chains 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.125361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106096 restraints weight = 5059.187| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.52 r_work: 0.2917 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4531 Z= 0.096 Angle : 0.452 7.211 6140 Z= 0.226 Chirality : 0.038 0.149 695 Planarity : 0.004 0.060 770 Dihedral : 4.313 27.902 597 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.46 % Allowed : 20.08 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.41 (0.37), residues: 536 helix: 2.25 (0.32), residues: 275 sheet: -1.97 (0.87), residues: 26 loop : -0.28 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 122 TYR 0.008 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 4531) covalent geometry : angle 0.45220 ( 6140) hydrogen bonds : bond 0.02942 ( 210) hydrogen bonds : angle 4.16272 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.218 Fit side-chains REVERT: A 224 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 277 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 378 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7905 (mpt180) REVERT: B 12 GLU cc_start: 0.6899 (tp30) cc_final: 0.6235 (tp30) REVERT: B 34 LYS cc_start: 0.8643 (ptmm) cc_final: 0.8110 (ptpt) REVERT: B 131 GLN cc_start: 0.8733 (mt0) cc_final: 0.8001 (mp10) REVERT: B 178 LYS cc_start: 0.7717 (mtpp) cc_final: 0.7437 (tttp) REVERT: B 242 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7183 (mtmm) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.0919 time to fit residues: 11.3765 Evaluate side-chains 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105805 restraints weight = 5077.981| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.55 r_work: 0.2909 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4531 Z= 0.100 Angle : 0.465 7.632 6140 Z= 0.229 Chirality : 0.038 0.149 695 Planarity : 0.004 0.049 770 Dihedral : 4.178 28.342 596 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.46 % Allowed : 20.70 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.41 (0.37), residues: 536 helix: 2.23 (0.32), residues: 276 sheet: -1.99 (0.88), residues: 26 loop : -0.27 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 122 TYR 0.008 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4531) covalent geometry : angle 0.46498 ( 6140) hydrogen bonds : bond 0.02908 ( 210) hydrogen bonds : angle 4.13503 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 378 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7895 (mpt180) REVERT: B 12 GLU cc_start: 0.6922 (tp30) cc_final: 0.6250 (tp30) REVERT: B 34 LYS cc_start: 0.8652 (ptmm) cc_final: 0.8107 (ptpt) REVERT: B 131 GLN cc_start: 0.8715 (mt0) cc_final: 0.7990 (mp10) REVERT: B 178 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7433 (tttp) REVERT: B 242 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7173 (mtmm) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.0848 time to fit residues: 10.0540 Evaluate side-chains 93 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.0050 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105577 restraints weight = 5102.178| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.55 r_work: 0.2903 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4531 Z= 0.103 Angle : 0.461 8.161 6140 Z= 0.229 Chirality : 0.038 0.147 695 Planarity : 0.004 0.043 770 Dihedral : 4.172 28.510 596 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.25 % Allowed : 21.93 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.39 (0.37), residues: 536 helix: 2.24 (0.32), residues: 276 sheet: -2.01 (0.88), residues: 26 loop : -0.30 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 250 TYR 0.008 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4531) covalent geometry : angle 0.46057 ( 6140) hydrogen bonds : bond 0.02918 ( 210) hydrogen bonds : angle 4.10063 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 378 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7901 (mpt180) REVERT: B 12 GLU cc_start: 0.6973 (tp30) cc_final: 0.6318 (tp30) REVERT: B 34 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8124 (ptpt) REVERT: B 131 GLN cc_start: 0.8715 (mt0) cc_final: 0.8027 (mp10) REVERT: B 172 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: B 178 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7441 (tttp) REVERT: B 242 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7177 (mtmm) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.0962 time to fit residues: 11.5119 Evaluate side-chains 93 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 172 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.125023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.105704 restraints weight = 5042.023| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.52 r_work: 0.2912 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4531 Z= 0.102 Angle : 0.466 8.715 6140 Z= 0.232 Chirality : 0.038 0.147 695 Planarity : 0.004 0.040 770 Dihedral : 4.168 28.564 596 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.25 % Allowed : 21.11 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.38 (0.37), residues: 536 helix: 2.23 (0.32), residues: 276 sheet: -2.01 (0.88), residues: 26 loop : -0.31 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.008 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.007 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4531) covalent geometry : angle 0.46603 ( 6140) hydrogen bonds : bond 0.02928 ( 210) hydrogen bonds : angle 4.08858 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.184 Fit side-chains REVERT: A 179 HIS cc_start: 0.7731 (t-90) cc_final: 0.6488 (m-70) REVERT: A 277 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 378 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7899 (mpt180) REVERT: B 12 GLU cc_start: 0.6983 (tp30) cc_final: 0.6334 (tp30) REVERT: B 34 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8130 (ptpt) REVERT: B 131 GLN cc_start: 0.8743 (mt0) cc_final: 0.7963 (mp10) REVERT: B 172 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 178 LYS cc_start: 0.7715 (mtpp) cc_final: 0.7439 (tttp) REVERT: B 242 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7157 (mtmm) outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.0907 time to fit residues: 10.7743 Evaluate side-chains 96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 235 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.0050 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 24 optimal weight: 0.0470 chunk 2 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 chunk 20 optimal weight: 6.9990 overall best weight: 0.0506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.131875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.113104 restraints weight = 5084.182| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.48 r_work: 0.3017 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4531 Z= 0.082 Angle : 0.448 8.907 6140 Z= 0.223 Chirality : 0.037 0.147 695 Planarity : 0.004 0.043 770 Dihedral : 3.838 25.897 596 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.23 % Allowed : 22.54 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.62 (0.37), residues: 536 helix: 2.41 (0.32), residues: 277 sheet: -1.72 (1.05), residues: 16 loop : -0.29 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 250 TYR 0.007 0.001 TYR A 199 PHE 0.008 0.001 PHE B 152 TRP 0.007 0.001 TRP A 372 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 4531) covalent geometry : angle 0.44771 ( 6140) hydrogen bonds : bond 0.02411 ( 210) hydrogen bonds : angle 3.95636 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.179 Fit side-chains REVERT: A 179 HIS cc_start: 0.7585 (t-90) cc_final: 0.6472 (m-70) REVERT: A 180 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 277 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 330 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7573 (mp0) REVERT: A 378 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7889 (mtm-85) REVERT: A 385 GLU cc_start: 0.7631 (tp30) cc_final: 0.7423 (pp20) REVERT: A 400 LYS cc_start: 0.8365 (mtpp) cc_final: 0.7983 (mtpp) REVERT: A 425 ASN cc_start: 0.7817 (p0) cc_final: 0.7573 (p0) REVERT: B 12 GLU cc_start: 0.6873 (tp30) cc_final: 0.6275 (tp30) REVERT: B 34 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8055 (ptpt) REVERT: B 131 GLN cc_start: 0.8634 (mt0) cc_final: 0.7999 (mp10) REVERT: B 178 LYS cc_start: 0.7347 (mtpp) cc_final: 0.7054 (tttp) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.0916 time to fit residues: 10.6948 Evaluate side-chains 88 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.126174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.106524 restraints weight = 5041.274| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.55 r_work: 0.2924 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.027 4531 Z= 0.116 Angle : 0.485 10.393 6140 Z= 0.237 Chirality : 0.039 0.147 695 Planarity : 0.004 0.039 770 Dihedral : 3.795 19.873 594 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.84 % Allowed : 21.72 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.49 (0.37), residues: 536 helix: 2.32 (0.32), residues: 276 sheet: -1.95 (0.88), residues: 26 loop : -0.25 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.008 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.006 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4531) covalent geometry : angle 0.48541 ( 6140) hydrogen bonds : bond 0.02920 ( 210) hydrogen bonds : angle 4.00741 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 179 HIS cc_start: 0.7695 (t-90) cc_final: 0.6488 (m-70) REVERT: A 180 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 378 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7760 (mpt180) REVERT: B 12 GLU cc_start: 0.6897 (tp30) cc_final: 0.6247 (tp30) REVERT: B 34 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8136 (ptpt) REVERT: B 107 TYR cc_start: 0.9233 (m-10) cc_final: 0.8981 (m-10) REVERT: B 131 GLN cc_start: 0.8691 (mt0) cc_final: 0.7949 (mp10) REVERT: B 172 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 178 LYS cc_start: 0.7544 (mtpp) cc_final: 0.7250 (tttp) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.0938 time to fit residues: 10.2487 Evaluate side-chains 89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 172 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.108129 restraints weight = 5065.074| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.56 r_work: 0.2941 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4531 Z= 0.091 Angle : 0.465 10.548 6140 Z= 0.228 Chirality : 0.038 0.146 695 Planarity : 0.004 0.041 770 Dihedral : 3.737 18.332 594 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.43 % Allowed : 22.34 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.53 (0.37), residues: 536 helix: 2.32 (0.32), residues: 276 sheet: -1.86 (1.02), residues: 16 loop : -0.29 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 250 TYR 0.008 0.001 TYR A 413 PHE 0.010 0.001 PHE B 152 TRP 0.006 0.001 TRP A 372 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 4531) covalent geometry : angle 0.46458 ( 6140) hydrogen bonds : bond 0.02696 ( 210) hydrogen bonds : angle 3.96726 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1337.44 seconds wall clock time: 23 minutes 40.45 seconds (1420.45 seconds total)