Starting phenix.real_space_refine on Wed May 14 09:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsr_18640/05_2025/8qsr_18640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsr_18640/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsr_18640/05_2025/8qsr_18640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsr_18640/05_2025/8qsr_18640.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsr_18640/05_2025/8qsr_18640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsr_18640/05_2025/8qsr_18640.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.42, per 1000 atoms: 0.46 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: 3.01 Conformation dependent library (CDL) restraints added in 891.6 milliseconds 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: 0.83 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: 4.11 Time building geometry restraints manager: 3.59 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: 0.03 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: 0.710 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: 0.190 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.040 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 39 HIS 0.002 0.001 HIS B 212 PHE 0.018 0.001 PHE A 256 TYR 0.007 0.001 TYR B 312 ARG 0.002 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.12467 ( 422) hydrogen bonds : angle 6.74861 ( 1242) covalent geometry : bond 0.00391 ( 5976) covalent geometry : angle 0.57013 ( 8142) *********************** 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 : 0.878 Fit side-chains revert: symmetry clash 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: 1.7138 time to fit residues: 296.7347 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 : 0.770 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.162483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153593 restraints weight = 21157.255| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.38 r_work: 0.4001 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2287 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= 0.191 Angle : 0.578 5.340 8142 Z= 0.311 Chirality : 0.043 0.134 938 Planarity : 0.005 0.045 1010 Dihedral : 5.277 70.261 857 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 10.00 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.31), residues: 762 helix: 1.67 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 39 HIS 0.003 0.001 HIS A 339 PHE 0.015 0.002 PHE B 195 TYR 0.019 0.002 TYR A 312 ARG 0.005 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 422) hydrogen bonds : angle 5.37798 ( 1242) covalent geometry : bond 0.00422 ( 5976) covalent geometry : angle 0.57828 ( 8142) *********************** 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 : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6236 (mpt) REVERT: B 344 PHE cc_start: 0.6116 (t80) cc_final: 0.5864 (t80) outliers start: 12 outliers final: 2 residues processed: 136 average time/residue: 1.9053 time to fit residues: 274.7795 Evaluate side-chains 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.163233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.154448 restraints weight = 21379.997| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.38 r_work: 0.4009 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2549 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= 0.137 Angle : 0.519 5.109 8142 Z= 0.274 Chirality : 0.040 0.119 938 Planarity : 0.005 0.042 1010 Dihedral : 4.912 61.775 855 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.53 % Allowed : 11.69 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.31), residues: 762 helix: 1.78 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 0.03 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 39 HIS 0.003 0.001 HIS B 339 PHE 0.013 0.001 PHE B 195 TYR 0.022 0.001 TYR B 312 ARG 0.005 0.001 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 422) hydrogen bonds : angle 5.16474 ( 1242) covalent geometry : bond 0.00278 ( 5976) covalent geometry : angle 0.51868 ( 8142) *********************** 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 139 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8256 (t) cc_final: 0.6622 (t) REVERT: A 284 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6094 (mpm) REVERT: B 380 ASP cc_start: 0.7501 (t0) cc_final: 0.7300 (t0) outliers start: 9 outliers final: 2 residues processed: 132 average time/residue: 1.8665 time to fit residues: 261.7625 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 : 0.764 ------------------------------------------------------------------------------- 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 250 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.158373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149450 restraints weight = 21191.690| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.40 r_work: 0.3954 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5976 Z= 0.244 Angle : 0.586 5.513 8142 Z= 0.318 Chirality : 0.044 0.130 938 Planarity : 0.005 0.044 1010 Dihedral : 4.892 49.168 855 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.20 % Allowed : 11.53 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 762 helix: 1.33 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 0.19 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 39 HIS 0.005 0.001 HIS A 339 PHE 0.016 0.002 PHE B 195 TYR 0.019 0.002 TYR B 312 ARG 0.008 0.001 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.05541 ( 422) hydrogen bonds : angle 5.25128 ( 1242) covalent geometry : bond 0.00546 ( 5976) covalent geometry : angle 0.58644 ( 8142) *********************** 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 145 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7937 (mm) REVERT: A 280 VAL cc_start: 0.8379 (t) cc_final: 0.6935 (t) REVERT: A 284 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.5971 (mpm) REVERT: A 344 PHE cc_start: 0.6712 (t80) cc_final: 0.6488 (t80) REVERT: A 380 ASP cc_start: 0.7508 (t0) cc_final: 0.7200 (t0) REVERT: B 380 ASP cc_start: 0.7646 (t0) cc_final: 0.7379 (t0) outliers start: 13 outliers final: 3 residues processed: 138 average time/residue: 1.7308 time to fit residues: 254.9204 Evaluate side-chains 134 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 284 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 215 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.159328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150414 restraints weight = 21176.831| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.41 r_work: 0.3960 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5976 Z= 0.176 Angle : 0.541 5.202 8142 Z= 0.290 Chirality : 0.042 0.124 938 Planarity : 0.005 0.043 1010 Dihedral : 4.586 40.935 855 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.86 % Allowed : 13.39 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.31), residues: 762 helix: 1.42 (0.22), residues: 518 sheet: None (None), residues: 0 loop : 0.38 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 172 HIS 0.005 0.001 HIS B 315 PHE 0.013 0.001 PHE B 195 TYR 0.016 0.002 TYR B 312 ARG 0.004 0.001 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 422) hydrogen bonds : angle 5.11938 ( 1242) covalent geometry : bond 0.00376 ( 5976) covalent geometry : angle 0.54080 ( 8142) *********************** 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 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.6187 (t70) REVERT: A 344 PHE cc_start: 0.6723 (t80) cc_final: 0.6400 (t80) REVERT: A 380 ASP cc_start: 0.7526 (t0) cc_final: 0.7190 (t0) REVERT: B 312 TYR cc_start: 0.7596 (t80) cc_final: 0.7380 (t80) REVERT: B 380 ASP cc_start: 0.7680 (t0) cc_final: 0.7393 (t0) outliers start: 11 outliers final: 1 residues processed: 131 average time/residue: 1.8180 time to fit residues: 253.4687 Evaluate side-chains 128 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU 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 9 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.159436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.150421 restraints weight = 21346.773| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.43 r_work: 0.3961 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5976 Z= 0.164 Angle : 0.531 5.304 8142 Z= 0.285 Chirality : 0.041 0.122 938 Planarity : 0.005 0.044 1010 Dihedral : 4.415 36.405 855 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.53 % Allowed : 13.90 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 762 helix: 1.48 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.49 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 39 HIS 0.003 0.001 HIS B 212 PHE 0.013 0.001 PHE B 195 TYR 0.015 0.002 TYR A 198 ARG 0.006 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 422) hydrogen bonds : angle 5.00973 ( 1242) covalent geometry : bond 0.00352 ( 5976) covalent geometry : angle 0.53066 ( 8142) *********************** 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 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6515 (OUTLIER) cc_final: 0.6177 (t70) REVERT: A 380 ASP cc_start: 0.7461 (t0) cc_final: 0.7105 (t0) REVERT: B 9 LEU cc_start: 0.7260 (mm) cc_final: 0.7016 (mt) REVERT: B 312 TYR cc_start: 0.7579 (t80) cc_final: 0.7375 (t80) REVERT: B 380 ASP cc_start: 0.7625 (t0) cc_final: 0.7311 (t0) outliers start: 9 outliers final: 0 residues processed: 134 average time/residue: 1.8011 time to fit residues: 256.9899 Evaluate side-chains 127 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 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 B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.150083 restraints weight = 21371.055| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.43 r_work: 0.3954 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3658 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= 0.171 Angle : 0.535 5.302 8142 Z= 0.286 Chirality : 0.041 0.120 938 Planarity : 0.005 0.042 1010 Dihedral : 4.016 17.509 852 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.36 % Allowed : 14.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 762 helix: 1.51 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.49 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 39 HIS 0.008 0.001 HIS B 315 PHE 0.013 0.001 PHE B 195 TYR 0.017 0.002 TYR B 312 ARG 0.003 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 422) hydrogen bonds : angle 4.97667 ( 1242) covalent geometry : bond 0.00366 ( 5976) covalent geometry : angle 0.53455 ( 8142) *********************** 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 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8418 (t) cc_final: 0.7115 (t) REVERT: A 284 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.5983 (mpm) REVERT: A 315 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6162 (t70) REVERT: A 380 ASP cc_start: 0.7519 (t0) cc_final: 0.7138 (t0) REVERT: B 9 LEU cc_start: 0.7339 (mm) cc_final: 0.7042 (mt) REVERT: B 315 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5887 (t-170) REVERT: B 380 ASP cc_start: 0.7656 (t0) cc_final: 0.7315 (t0) outliers start: 8 outliers final: 0 residues processed: 134 average time/residue: 1.8456 time to fit residues: 266.0094 Evaluate side-chains 129 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 315 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.160078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151115 restraints weight = 21352.933| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.43 r_work: 0.3968 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5976 Z= 0.139 Angle : 0.532 5.264 8142 Z= 0.285 Chirality : 0.040 0.119 938 Planarity : 0.005 0.043 1010 Dihedral : 3.970 17.870 852 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.19 % Allowed : 14.58 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.31), residues: 762 helix: 1.64 (0.22), residues: 520 sheet: None (None), residues: 0 loop : 0.68 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 269 HIS 0.022 0.001 HIS B 315 PHE 0.012 0.001 PHE B 195 TYR 0.024 0.002 TYR B 312 ARG 0.004 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 422) hydrogen bonds : angle 4.89803 ( 1242) covalent geometry : bond 0.00287 ( 5976) covalent geometry : angle 0.53188 ( 8142) *********************** 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 134 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6465 (OUTLIER) cc_final: 0.6163 (t70) REVERT: B 9 LEU cc_start: 0.7312 (mm) cc_final: 0.7043 (mt) REVERT: B 380 ASP cc_start: 0.7651 (t0) cc_final: 0.7296 (t0) outliers start: 7 outliers final: 1 residues processed: 131 average time/residue: 1.7984 time to fit residues: 250.8312 Evaluate side-chains 128 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 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 = 0.4134 r_free = 0.4134 target = 0.159053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.150104 restraints weight = 21290.561| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.41 r_work: 0.3955 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3823 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= 0.172 Angle : 0.543 5.395 8142 Z= 0.290 Chirality : 0.041 0.131 938 Planarity : 0.005 0.042 1010 Dihedral : 3.991 18.340 852 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.02 % Allowed : 15.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 762 helix: 1.60 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.50 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 39 HIS 0.002 0.001 HIS B 339 PHE 0.013 0.001 PHE B 195 TYR 0.018 0.002 TYR B 188 ARG 0.007 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 422) hydrogen bonds : angle 4.91861 ( 1242) covalent geometry : bond 0.00377 ( 5976) covalent geometry : angle 0.54327 ( 8142) *********************** 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 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.773 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: 0.6408 (OUTLIER) cc_final: 0.6129 (t70) REVERT: B 9 LEU cc_start: 0.7352 (mm) cc_final: 0.7051 (mt) outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 1.8087 time to fit residues: 248.0100 Evaluate side-chains 128 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.158474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149560 restraints weight = 21216.972| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.42 r_work: 0.3950 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5976 Z= 0.190 Angle : 0.555 5.431 8142 Z= 0.298 Chirality : 0.042 0.130 938 Planarity : 0.006 0.076 1010 Dihedral : 4.063 17.966 852 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.02 % Allowed : 15.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.31), residues: 762 helix: 1.54 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.45 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 172 HIS 0.002 0.001 HIS A 339 PHE 0.013 0.001 PHE B 195 TYR 0.017 0.002 TYR A 198 ARG 0.010 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 422) hydrogen bonds : angle 4.97040 ( 1242) covalent geometry : bond 0.00416 ( 5976) covalent geometry : angle 0.55505 ( 8142) ********************** 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 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.6142 (t70) REVERT: B 9 LEU cc_start: 0.7330 (mm) cc_final: 0.7046 (mt) outliers start: 6 outliers final: 1 residues processed: 132 average time/residue: 1.7947 time to fit residues: 252.3333 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 : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.158706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149826 restraints weight = 21290.765| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.42 r_work: 0.3951 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3962 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= 0.177 Angle : 0.550 5.388 8142 Z= 0.295 Chirality : 0.042 0.147 938 Planarity : 0.006 0.061 1010 Dihedral : 4.047 18.035 852 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.68 % Allowed : 15.76 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.31), residues: 762 helix: 1.59 (0.23), residues: 520 sheet: None (None), residues: 0 loop : 0.55 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 269 HIS 0.003 0.001 HIS A 315 PHE 0.014 0.001 PHE A 195 TYR 0.018 0.002 TYR B 188 ARG 0.007 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 422) hydrogen bonds : angle 4.93443 ( 1242) covalent geometry : bond 0.00385 ( 5976) covalent geometry : angle 0.54961 ( 8142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8319.46 seconds wall clock time: 142 minutes 49.26 seconds (8569.26 seconds total)