Starting phenix.real_space_refine on Tue Jul 29 20:01:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsr_18640/07_2025/8qsr_18640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsr_18640/07_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_18640/07_2025/8qsr_18640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsr_18640/07_2025/8qsr_18640.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsr_18640/07_2025/8qsr_18640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsr_18640/07_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-5711/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: 5.91, per 1000 atoms: 0.50 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: 3.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.01 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: 4.83 Time building geometry restraints manager: 4.00 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: 0.07 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: 0.830 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: 0.230 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.230 Find NCS groups from input model: 0.170 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- 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 : 0.771 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: 1.7588 time to fit residues: 304.6572 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 : 0.767 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.162482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153608 restraints weight = 21156.429| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.37 r_work: 0.4002 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2288 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 : 5.276 70.258 857 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 5.37796 ( 1242) covalent geometry : bond 0.00422 ( 5976) covalent geometry : angle 0.57826 ( 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 : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7294 (m-40) cc_final: 0.7090 (m110) 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: 0.5865 (t80) outliers start: 12 outliers final: 2 residues processed: 136 average time/residue: 1.9346 time to fit residues: 279.1353 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 : 0.775 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 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 212 HIS A 276 ASN A 350 ASN B 212 HIS B 276 ASN B 350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.162072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153260 restraints weight = 21320.038| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.38 r_work: 0.3994 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5976 Z= 0.163 Angle : 0.532 5.372 8142 Z= 0.282 Chirality : 0.041 0.114 938 Planarity : 0.005 0.041 1010 Dihedral : 4.922 59.408 855 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.69 % Allowed : 11.36 % Favored : 86.95 % 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: 1.68 (0.31), residues: 762 helix: 1.69 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.01 (0.43), residues: 246 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 0.023 0.002 TYR B 312 ARG 0.005 0.001 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.05014 ( 422) hydrogen bonds : angle 5.20620 ( 1242) covalent geometry : bond 0.00343 ( 5976) covalent geometry : angle 0.53198 ( 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 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8284 (t) cc_final: 0.6665 (t) REVERT: A 284 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.5986 (mpm) outliers start: 10 outliers final: 2 residues processed: 131 average time/residue: 1.9331 time to fit residues: 268.9181 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 : 0.788 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.159308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.150323 restraints weight = 21251.835| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.42 r_work: 0.3962 rms_B_bonded: 1.67 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: 0.7270 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5976 Z= 0.208 Angle : 0.559 5.397 8142 Z= 0.300 Chirality : 0.042 0.122 938 Planarity : 0.005 0.044 1010 Dihedral : 4.807 48.193 855 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.37 % Allowed : 11.69 % Favored : 85.93 % 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: 1.51 (0.31), residues: 762 helix: 1.44 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 0.23 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 39 HIS 0.003 0.001 HIS A 339 PHE 0.015 0.002 PHE B 195 TYR 0.017 0.002 TYR B 312 ARG 0.008 0.001 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 422) hydrogen bonds : angle 5.15939 ( 1242) covalent geometry : bond 0.00462 ( 5976) covalent geometry : angle 0.55852 ( 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 144 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7897 (mm) REVERT: A 344 PHE cc_start: 0.6675 (t80) cc_final: 0.6474 (t80) REVERT: B 215 ASN cc_start: 0.6988 (m-40) cc_final: 0.6580 (m110) outliers start: 14 outliers final: 3 residues processed: 136 average time/residue: 1.7919 time to fit residues: 259.6762 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 210 LEU 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: 0.7980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 315 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.159330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.150380 restraints weight = 21149.952| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.42 r_work: 0.3959 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3307 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= 0.185 Angle : 0.542 5.278 8142 Z= 0.290 Chirality : 0.041 0.127 938 Planarity : 0.005 0.042 1010 Dihedral : 4.557 40.830 855 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.78 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: 1.57 (0.31), residues: 762 helix: 1.44 (0.22), residues: 518 sheet: None (None), residues: 0 loop : 0.36 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 269 HIS 0.004 0.001 HIS B 315 PHE 0.014 0.001 PHE B 195 TYR 0.018 0.002 TYR B 312 ARG 0.003 0.001 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 422) hydrogen bonds : angle 5.09760 ( 1242) covalent geometry : bond 0.00397 ( 5976) covalent geometry : angle 0.54187 ( 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 141 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.6267 (t70) REVERT: A 344 PHE cc_start: 0.6718 (t80) cc_final: 0.6470 (t80) REVERT: A 380 ASP cc_start: 0.7543 (t0) cc_final: 0.7219 (t0) REVERT: B 215 ASN cc_start: 0.6993 (m-40) cc_final: 0.6781 (m110) REVERT: B 312 TYR cc_start: 0.7602 (t80) cc_final: 0.7386 (t80) outliers start: 11 outliers final: 2 residues processed: 134 average time/residue: 1.9440 time to fit residues: 277.2053 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 : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 46 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.160362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151388 restraints weight = 21399.297| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.43 r_work: 0.3972 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5976 Z= 0.140 Angle : 0.525 5.204 8142 Z= 0.280 Chirality : 0.041 0.124 938 Planarity : 0.005 0.045 1010 Dihedral : 4.356 37.511 855 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.53 % Allowed : 14.41 % 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: 1.84 (0.31), residues: 762 helix: 1.57 (0.22), residues: 520 sheet: None (None), residues: 0 loop : 0.66 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 269 HIS 0.003 0.001 HIS B 212 PHE 0.013 0.001 PHE B 195 TYR 0.016 0.001 TYR B 312 ARG 0.004 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 422) hydrogen bonds : angle 4.96274 ( 1242) covalent geometry : bond 0.00291 ( 5976) covalent geometry : angle 0.52495 ( 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 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.6183 (t70) REVERT: A 380 ASP cc_start: 0.7445 (t0) cc_final: 0.7101 (t0) REVERT: B 9 LEU cc_start: 0.7315 (mm) cc_final: 0.7032 (mt) REVERT: B 312 TYR cc_start: 0.7569 (t80) cc_final: 0.7357 (t80) outliers start: 9 outliers final: 1 residues processed: 132 average time/residue: 2.3127 time to fit residues: 326.4627 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 : 2.076 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.159264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150232 restraints weight = 21406.831| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.43 r_work: 0.3957 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3628 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= 0.173 Angle : 0.537 5.326 8142 Z= 0.288 Chirality : 0.041 0.121 938 Planarity : 0.005 0.043 1010 Dihedral : 3.977 17.176 852 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.19 % Allowed : 15.42 % 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 (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 : 0.47 (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 0.019 0.002 TYR B 312 ARG 0.004 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 422) hydrogen bonds : angle 4.98024 ( 1242) covalent geometry : bond 0.00375 ( 5976) covalent geometry : angle 0.53663 ( 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 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.6223 (t70) REVERT: B 9 LEU cc_start: 0.7331 (mm) cc_final: 0.7056 (mt) REVERT: B 315 HIS cc_start: 0.6111 (OUTLIER) cc_final: 0.5889 (t-170) outliers start: 7 outliers final: 1 residues processed: 133 average time/residue: 1.9741 time to fit residues: 279.9299 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 250 LEU 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: 0.7980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.160189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.151207 restraints weight = 21396.834| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.43 r_work: 0.3969 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5976 Z= 0.140 Angle : 0.535 5.217 8142 Z= 0.286 Chirality : 0.040 0.120 938 Planarity : 0.005 0.043 1010 Dihedral : 3.938 17.516 852 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.19 % Allowed : 15.25 % 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: 1.88 (0.31), residues: 762 helix: 1.61 (0.22), residues: 520 sheet: None (None), residues: 0 loop : 0.64 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 269 HIS 0.021 0.001 HIS B 315 PHE 0.012 0.001 PHE B 195 TYR 0.024 0.002 TYR B 312 ARG 0.003 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 422) hydrogen bonds : angle 4.90844 ( 1242) covalent geometry : bond 0.00291 ( 5976) covalent geometry : angle 0.53465 ( 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 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.5973 (mpm) REVERT: A 315 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.6164 (t70) REVERT: B 9 LEU cc_start: 0.7318 (mm) cc_final: 0.7030 (mt) outliers start: 7 outliers final: 1 residues processed: 131 average time/residue: 1.9696 time to fit residues: 275.3952 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 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 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 = 0.4133 r_free = 0.4133 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.150194 restraints weight = 21337.717| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.39 r_work: 0.3957 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5976 Z= 0.182 Angle : 0.551 5.508 8142 Z= 0.296 Chirality : 0.042 0.124 938 Planarity : 0.006 0.066 1010 Dihedral : 4.002 17.704 852 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.19 % Allowed : 15.76 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : 0.46 (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 B 212 PHE 0.013 0.001 PHE B 195 TYR 0.019 0.002 TYR B 312 ARG 0.010 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 422) hydrogen bonds : angle 4.95926 ( 1242) covalent geometry : bond 0.00401 ( 5976) covalent geometry : angle 0.55107 ( 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 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.6212 (t70) REVERT: B 9 LEU cc_start: 0.7353 (mm) cc_final: 0.7074 (mt) outliers start: 7 outliers final: 1 residues processed: 131 average time/residue: 1.8399 time to fit residues: 256.4338 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 : 0.890 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.159301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150380 restraints weight = 21285.183| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.42 r_work: 0.3961 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5976 Z= 0.154 Angle : 0.545 5.985 8142 Z= 0.291 Chirality : 0.041 0.123 938 Planarity : 0.006 0.057 1010 Dihedral : 3.963 18.065 852 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.34 % Allowed : 16.95 % Favored : 82.71 % 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: 1.89 (0.31), residues: 762 helix: 1.64 (0.23), residues: 520 sheet: None (None), residues: 0 loop : 0.59 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 269 HIS 0.002 0.001 HIS A 339 PHE 0.012 0.001 PHE B 195 TYR 0.017 0.002 TYR A 188 ARG 0.008 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 422) hydrogen bonds : angle 4.90325 ( 1242) covalent geometry : bond 0.00329 ( 5976) covalent geometry : angle 0.54516 ( 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 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.6076 (t70) REVERT: B 9 LEU cc_start: 0.7336 (mm) cc_final: 0.7048 (mt) outliers start: 2 outliers final: 1 residues processed: 130 average time/residue: 1.8227 time to fit residues: 252.2587 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 : 0.757 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.159043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.150132 restraints weight = 21323.781| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.42 r_work: 0.3956 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3948 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 : 0.551 5.731 8142 Z= 0.295 Chirality : 0.041 0.145 938 Planarity : 0.006 0.066 1010 Dihedral : 3.982 17.929 852 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.68 % Allowed : 16.27 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.31), residues: 762 helix: 1.61 (0.23), residues: 520 sheet: None (None), residues: 0 loop : 0.56 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 172 HIS 0.003 0.001 HIS B 212 PHE 0.014 0.001 PHE A 195 TYR 0.018 0.002 TYR B 188 ARG 0.009 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 422) hydrogen bonds : angle 4.91240 ( 1242) covalent geometry : bond 0.00365 ( 5976) covalent geometry : angle 0.55112 ( 8142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9117.44 seconds wall clock time: 159 minutes 9.80 seconds (9549.80 seconds total)