Starting phenix.real_space_refine on Sat Aug 23 11:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsr_18640/08_2025/8qsr_18640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsr_18640/08_2025/8qsr_18640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qsr_18640/08_2025/8qsr_18640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsr_18640/08_2025/8qsr_18640.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qsr_18640/08_2025/8qsr_18640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsr_18640/08_2025/8qsr_18640.map" } resolution = 2.56 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= 0.001 sd= 0.016 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 S 28 5.16 5 C 3870 2.51 5 N 932 2.21 5 O 978 1.98 5 H 5938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5861 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain: "B" Number of atoms: 5861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5861 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.14 Number of scatterers: 11746 At special positions: 0 Unit cell: (113.197, 76.4325, 71.595, 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 28 16.00 O 978 8.00 N 932 7.00 C 3870 6.00 H 5938 1.00 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: 1.12 Conformation dependent library (CDL) restraints added in 339.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 84.7% alpha, 0.5% 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 4 through 22 Proline residue: A 19 - end of helix removed outlier: 3.813A pdb=" N VAL A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 36 removed outlier: 4.033A pdb=" N ALA A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.629A pdb=" N ASN A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 75 through 102 Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 117 through 136 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.573A pdb=" N GLY A 145 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.912A pdb=" N ARG A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 152 through 189 Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 221 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 258 removed outlier: 4.179A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 294 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.671A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 348 through 351 Processing helix chain 'A' and resid 355 through 380 removed outlier: 3.916A pdb=" N ILE A 359 " --> pdb=" O TRP A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 22 Proline residue: B 19 - end of helix removed outlier: 3.812A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 4.033A pdb=" N ALA B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.628A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 Processing helix chain 'B' and resid 75 through 102 removed outlier: 3.503A pdb=" N ALA B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 136 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.573A pdb=" N GLY B 145 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 removed outlier: 3.920A pdb=" N ARG B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 152 through 189 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 190 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 221 Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 258 removed outlier: 4.180A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 277 through 294 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 308 through 330 removed outlier: 3.671A pdb=" N PHE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 355 through 380 removed outlier: 3.917A pdb=" N ILE B 359 " --> pdb=" O TRP B 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA2, first strand: chain 'B' and resid 225 through 226 422 hydrogen bonds defined for protein. 1242 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: 1.82 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5934 1.03 - 1.22: 14 1.22 - 1.42: 2499 1.42 - 1.61: 3415 1.61 - 1.81: 52 Bond restraints: 11914 Sorted by residual: bond pdb=" NE ARG A 151 " pdb=" HE ARG A 151 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG B 151 " pdb=" HE ARG B 151 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C GLU A 202 " pdb=" O GLU A 202 " ideal model delta sigma weight residual 1.236 1.181 0.056 1.15e-02 7.56e+03 2.33e+01 bond pdb=" C GLU A 298 " pdb=" O GLU A 298 " ideal model delta sigma weight residual 1.238 1.188 0.050 1.28e-02 6.10e+03 1.53e+01 bond pdb=" NZ LYS B 91 " pdb=" HZ3 LYS B 91 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.24e+01 ... (remaining 11909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 18603 1.25 - 2.50: 1740 2.50 - 3.74: 1130 3.74 - 4.99: 88 4.99 - 6.24: 51 Bond angle restraints: 21612 Sorted by residual: angle pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" N GLY A 76 " ideal model delta sigma weight residual 116.28 119.99 -3.71 1.26e+00 6.30e-01 8.66e+00 angle pdb=" C ASP B 75 " pdb=" N GLY B 76 " pdb=" CA GLY B 76 " ideal model delta sigma weight residual 120.22 123.90 -3.68 1.27e+00 6.20e-01 8.41e+00 angle pdb=" CA ASP B 75 " pdb=" C ASP B 75 " pdb=" N GLY B 76 " ideal model delta sigma weight residual 116.28 119.82 -3.54 1.26e+00 6.30e-01 7.88e+00 angle pdb=" C ASP A 75 " pdb=" N GLY A 76 " pdb=" CA GLY A 76 " ideal model delta sigma weight residual 120.22 123.67 -3.45 1.27e+00 6.20e-01 7.40e+00 angle pdb=" C GLU A 202 " pdb=" CA GLU A 202 " pdb=" CB GLU A 202 " ideal model delta sigma weight residual 110.88 106.81 4.07 1.57e+00 4.06e-01 6.72e+00 ... (remaining 21607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 5192 15.76 - 31.52: 252 31.52 - 47.28: 97 47.28 - 63.04: 124 63.04 - 78.80: 3 Dihedral angle restraints: 5668 sinusoidal: 2990 harmonic: 2678 Sorted by residual: dihedral pdb=" CA ILE A 171 " pdb=" C ILE A 171 " pdb=" N TRP A 172 " pdb=" CA TRP A 172 " ideal model delta harmonic sigma weight residual 180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE B 171 " pdb=" C ILE B 171 " pdb=" N TRP B 172 " pdb=" CA TRP B 172 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 172 " pdb=" C TRP A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 796 0.065 - 0.130: 138 0.130 - 0.194: 3 0.194 - 0.259: 0 0.259 - 0.324: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA GLU A 298 " pdb=" N GLU A 298 " pdb=" C GLU A 298 " pdb=" CB GLU A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLN A 219 " pdb=" N GLN A 219 " pdb=" C GLN A 219 " pdb=" CB GLN A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 935 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 256 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PHE A 256 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE A 256 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 257 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 256 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C PHE B 256 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE B 256 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 257 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 219 " 0.012 2.00e-02 2.50e+03 1.28e-02 2.44e+00 pdb=" CD GLN A 219 " -0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN A 219 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A 219 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 219 " -0.018 2.00e-02 2.50e+03 pdb="HE22 GLN A 219 " 0.019 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 358 2.14 - 2.75: 22490 2.75 - 3.37: 35500 3.37 - 3.98: 45493 3.98 - 4.60: 72667 Nonbonded interactions: 176508 Sorted by model distance: nonbonded pdb=" O ALA B 68 " pdb=" HG1 THR B 72 " model vdw 1.524 2.450 nonbonded pdb=" O ALA A 68 " pdb=" HG1 THR A 72 " model vdw 1.524 2.450 nonbonded pdb=" O ILE B 300 " pdb=" HG SER B 303 " model vdw 1.534 2.450 nonbonded pdb=" O ILE A 300 " pdb=" HG SER A 303 " model vdw 1.534 2.450 nonbonded pdb=" O ALA A 129 " pdb="HD22 ASN A 133 " model vdw 1.604 2.450 ... (remaining 176503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:5.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5976 Z= 0.231 Angle : 0.570 5.555 8142 Z= 0.321 Chirality : 0.043 0.324 938 Planarity : 0.004 0.026 1010 Dihedral : 10.417 78.799 2082 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.34 % Allowed : 2.20 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.31), residues: 762 helix: 1.96 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.007 0.001 TYR B 312 PHE 0.018 0.001 PHE A 256 TRP 0.005 0.001 TRP A 39 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5976) covalent geometry : angle 0.57013 ( 8142) hydrogen bonds : bond 0.12467 ( 422) hydrogen bonds : angle 6.74861 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 162 average time/residue: 0.7481 time to fit residues: 129.2318 Evaluate side-chains 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain B residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 215 ASN A 276 ASN A 350 ASN B 212 HIS B 276 ASN B 350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153597 restraints weight = 21379.630| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.42 r_work: 0.4000 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5976 Z= 0.191 Angle : 0.578 5.438 8142 Z= 0.310 Chirality : 0.043 0.146 938 Planarity : 0.005 0.044 1010 Dihedral : 5.212 65.364 857 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 9.83 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.31), residues: 762 helix: 1.67 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -0.00 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.021 0.002 TYR B 312 PHE 0.017 0.002 PHE B 195 TRP 0.006 0.001 TRP A 39 HIS 0.003 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 5976) covalent geometry : angle 0.57839 ( 8142) hydrogen bonds : bond 0.05249 ( 422) hydrogen bonds : angle 5.42039 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6294 (mpt) REVERT: B 344 PHE cc_start: 0.6177 (t80) cc_final: 0.5879 (t80) outliers start: 12 outliers final: 3 residues processed: 136 average time/residue: 0.8478 time to fit residues: 122.1721 Evaluate side-chains 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 350 ASN B 212 HIS B 276 ASN B 350 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.161606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.152654 restraints weight = 21467.603| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.40 r_work: 0.3988 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5976 Z= 0.179 Angle : 0.541 5.266 8142 Z= 0.289 Chirality : 0.042 0.123 938 Planarity : 0.005 0.041 1010 Dihedral : 4.939 56.359 855 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.69 % Allowed : 11.02 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.31), residues: 762 helix: 1.55 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 0.29 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.021 0.002 TYR B 312 PHE 0.014 0.001 PHE B 195 TRP 0.005 0.001 TRP B 39 HIS 0.002 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5976) covalent geometry : angle 0.54116 ( 8142) hydrogen bonds : bond 0.05128 ( 422) hydrogen bonds : angle 5.27135 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8321 (t) cc_final: 0.6697 (t) REVERT: A 284 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6115 (mpm) REVERT: A 380 ASP cc_start: 0.7338 (t0) cc_final: 0.7124 (t0) REVERT: B 380 ASP cc_start: 0.7530 (t0) cc_final: 0.7326 (t0) outliers start: 10 outliers final: 3 residues processed: 131 average time/residue: 0.8738 time to fit residues: 121.1764 Evaluate side-chains 128 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 350 ASN B 276 ASN B 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151335 restraints weight = 21256.986| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.44 r_work: 0.3971 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5976 Z= 0.183 Angle : 0.545 5.325 8142 Z= 0.290 Chirality : 0.042 0.125 938 Planarity : 0.005 0.043 1010 Dihedral : 4.797 49.368 855 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.86 % Allowed : 11.69 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.31), residues: 762 helix: 1.53 (0.23), residues: 516 sheet: None (None), residues: 0 loop : 0.24 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 151 TYR 0.015 0.002 TYR B 312 PHE 0.020 0.001 PHE A 344 TRP 0.005 0.001 TRP B 39 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5976) covalent geometry : angle 0.54462 ( 8142) hydrogen bonds : bond 0.05010 ( 422) hydrogen bonds : angle 5.12827 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 315 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6210 (t70) REVERT: B 9 LEU cc_start: 0.7209 (mm) cc_final: 0.6864 (mt) REVERT: B 215 ASN cc_start: 0.7016 (m-40) cc_final: 0.6677 (m110) REVERT: B 312 TYR cc_start: 0.7596 (t80) cc_final: 0.7386 (t80) REVERT: B 380 ASP cc_start: 0.7597 (t0) cc_final: 0.7338 (t0) outliers start: 11 outliers final: 1 residues processed: 136 average time/residue: 0.7897 time to fit residues: 114.0099 Evaluate side-chains 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 276 ASN A 350 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.161322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.152242 restraints weight = 21177.797| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.44 r_work: 0.3982 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5976 Z= 0.133 Angle : 0.517 5.190 8142 Z= 0.273 Chirality : 0.040 0.118 938 Planarity : 0.005 0.043 1010 Dihedral : 4.493 44.233 855 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.36 % Allowed : 14.24 % Favored : 84.41 % 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 aren not related in a simple way. whole: 1.78 (0.31), residues: 762 helix: 1.71 (0.22), residues: 518 sheet: None (None), residues: 0 loop : 0.14 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 151 TYR 0.014 0.001 TYR B 312 PHE 0.013 0.001 PHE B 195 TRP 0.004 0.001 TRP B 269 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5976) covalent geometry : angle 0.51655 ( 8142) hydrogen bonds : bond 0.04621 ( 422) hydrogen bonds : angle 4.99473 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 315 HIS cc_start: 0.6531 (OUTLIER) cc_final: 0.6179 (t70) REVERT: B 215 ASN cc_start: 0.6888 (m-40) cc_final: 0.6608 (m110) REVERT: B 312 TYR cc_start: 0.7546 (t80) cc_final: 0.7315 (t80) REVERT: B 380 ASP cc_start: 0.7622 (t0) cc_final: 0.7336 (t0) outliers start: 8 outliers final: 0 residues processed: 133 average time/residue: 0.8173 time to fit residues: 115.5615 Evaluate side-chains 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 22 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 276 ASN B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.158382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149492 restraints weight = 21382.557| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.41 r_work: 0.3957 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5976 Z= 0.207 Angle : 0.560 5.361 8142 Z= 0.300 Chirality : 0.042 0.125 938 Planarity : 0.005 0.045 1010 Dihedral : 4.007 17.245 852 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.69 % Allowed : 14.41 % Favored : 83.90 % 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 aren not related in a simple way. whole: 1.60 (0.31), residues: 762 helix: 1.42 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.45 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.017 0.002 TYR A 198 PHE 0.014 0.001 PHE B 195 TRP 0.006 0.001 TRP B 39 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5976) covalent geometry : angle 0.55961 ( 8142) hydrogen bonds : bond 0.05151 ( 422) hydrogen bonds : angle 5.07902 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6543 (OUTLIER) cc_final: 0.6217 (t70) REVERT: A 380 ASP cc_start: 0.7441 (t0) cc_final: 0.7136 (t0) REVERT: B 9 LEU cc_start: 0.7363 (mm) cc_final: 0.7077 (mt) REVERT: B 380 ASP cc_start: 0.7613 (t0) cc_final: 0.7307 (t0) outliers start: 10 outliers final: 1 residues processed: 134 average time/residue: 0.7749 time to fit residues: 110.3663 Evaluate side-chains 129 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 60 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN A 350 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151789 restraints weight = 21342.449| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.43 r_work: 0.3977 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5976 Z= 0.126 Angle : 0.511 5.167 8142 Z= 0.273 Chirality : 0.040 0.118 938 Planarity : 0.005 0.043 1010 Dihedral : 3.860 17.412 852 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.02 % Allowed : 14.92 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.31), residues: 762 helix: 1.75 (0.22), residues: 520 sheet: None (None), residues: 0 loop : 0.41 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 277 TYR 0.017 0.001 TYR B 312 PHE 0.012 0.001 PHE B 195 TRP 0.005 0.001 TRP A 269 HIS 0.007 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5976) covalent geometry : angle 0.51138 ( 8142) hydrogen bonds : bond 0.04512 ( 422) hydrogen bonds : angle 4.88938 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 LEU cc_start: 0.7292 (mm) cc_final: 0.7037 (mt) REVERT: B 312 TYR cc_start: 0.7540 (t80) cc_final: 0.7323 (t80) REVERT: B 380 ASP cc_start: 0.7629 (t0) cc_final: 0.7293 (t0) outliers start: 6 outliers final: 1 residues processed: 130 average time/residue: 0.7974 time to fit residues: 110.1010 Evaluate side-chains 125 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN A 350 ASN B 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.159696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.150815 restraints weight = 21243.470| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.40 r_work: 0.3967 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5976 Z= 0.162 Angle : 0.527 5.305 8142 Z= 0.281 Chirality : 0.041 0.118 938 Planarity : 0.005 0.042 1010 Dihedral : 3.903 17.709 852 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.19 % Allowed : 15.08 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.31), residues: 762 helix: 1.64 (0.23), residues: 522 sheet: None (None), residues: 0 loop : 0.54 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 151 TYR 0.017 0.002 TYR B 188 PHE 0.013 0.001 PHE B 195 TRP 0.004 0.001 TRP B 172 HIS 0.002 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5976) covalent geometry : angle 0.52709 ( 8142) hydrogen bonds : bond 0.04689 ( 422) hydrogen bonds : angle 4.90014 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.6228 (t70) REVERT: B 9 LEU cc_start: 0.7330 (mm) cc_final: 0.7026 (mt) REVERT: B 380 ASP cc_start: 0.7600 (t0) cc_final: 0.7250 (t0) outliers start: 7 outliers final: 1 residues processed: 134 average time/residue: 0.8453 time to fit residues: 120.5147 Evaluate side-chains 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN A 350 ASN B 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.159303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150281 restraints weight = 21209.045| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.42 r_work: 0.3958 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5976 Z= 0.167 Angle : 0.535 5.347 8142 Z= 0.286 Chirality : 0.041 0.122 938 Planarity : 0.005 0.041 1010 Dihedral : 3.942 17.982 852 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.85 % Allowed : 15.08 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.31), residues: 762 helix: 1.60 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.53 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.016 0.002 TYR A 198 PHE 0.013 0.001 PHE B 195 TRP 0.004 0.001 TRP B 269 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5976) covalent geometry : angle 0.53526 ( 8142) hydrogen bonds : bond 0.04680 ( 422) hydrogen bonds : angle 4.90603 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6380 (OUTLIER) cc_final: 0.6092 (t70) REVERT: B 9 LEU cc_start: 0.7333 (mm) cc_final: 0.7051 (mt) outliers start: 5 outliers final: 1 residues processed: 133 average time/residue: 0.8504 time to fit residues: 120.3165 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN B 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.159524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150484 restraints weight = 21310.570| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.42 r_work: 0.3960 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5976 Z= 0.159 Angle : 0.532 5.346 8142 Z= 0.284 Chirality : 0.041 0.129 938 Planarity : 0.006 0.072 1010 Dihedral : 3.930 17.615 852 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.85 % Allowed : 15.76 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.31), residues: 762 helix: 1.68 (0.23), residues: 520 sheet: None (None), residues: 0 loop : 0.69 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 277 TYR 0.016 0.002 TYR A 188 PHE 0.014 0.001 PHE A 195 TRP 0.004 0.001 TRP B 172 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5976) covalent geometry : angle 0.53196 ( 8142) hydrogen bonds : bond 0.04639 ( 422) hydrogen bonds : angle 4.87263 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6353 (OUTLIER) cc_final: 0.6056 (t70) REVERT: B 9 LEU cc_start: 0.7315 (mm) cc_final: 0.7025 (mt) outliers start: 5 outliers final: 0 residues processed: 130 average time/residue: 0.8088 time to fit residues: 111.8123 Evaluate side-chains 129 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN B 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.159421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150445 restraints weight = 21312.454| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.42 r_work: 0.3960 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5976 Z= 0.161 Angle : 0.532 5.370 8142 Z= 0.284 Chirality : 0.041 0.130 938 Planarity : 0.005 0.059 1010 Dihedral : 3.932 17.867 852 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.34 % Allowed : 16.27 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.31), residues: 762 helix: 1.66 (0.23), residues: 520 sheet: None (None), residues: 0 loop : 0.64 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 277 TYR 0.019 0.002 TYR B 188 PHE 0.012 0.001 PHE B 195 TRP 0.004 0.001 TRP B 172 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5976) covalent geometry : angle 0.53243 ( 8142) hydrogen bonds : bond 0.04642 ( 422) hydrogen bonds : angle 4.87841 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3938.07 seconds wall clock time: 67 minutes 15.27 seconds (4035.27 seconds total)