Starting phenix.real_space_refine on Wed Sep 17 05:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jj1_61514/09_2025/9jj1_61514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jj1_61514/09_2025/9jj1_61514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jj1_61514/09_2025/9jj1_61514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jj1_61514/09_2025/9jj1_61514.map" model { file = "/net/cci-nas-00/data/ceres_data/9jj1_61514/09_2025/9jj1_61514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jj1_61514/09_2025/9jj1_61514.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 36 5.16 5 C 3116 2.51 5 N 808 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4842 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2349 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain breaks: 1 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2349 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain breaks: 1 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {' ZN': 3, 'AV0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {' ZN': 3, 'AV0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4627 SG CYS B 379 37.218 59.325 24.387 1.00201.30 S ATOM 4652 SG CYS B 382 38.035 55.619 23.393 1.00189.33 S ATOM 2365 SG CYS B 55 30.256 32.900 22.811 1.00159.30 S ATOM 16 SG CYS A 55 33.504 51.244 22.319 1.00173.09 S ATOM 2278 SG CYS A 379 27.542 25.227 24.379 1.00199.48 S ATOM 2303 SG CYS A 382 26.600 28.826 23.148 1.00184.60 S Time building chain proxies: 1.50, per 1000 atoms: 0.31 Number of scatterers: 4842 At special positions: 0 Unit cell: (64.74, 85.49, 99.6, 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) Zn 6 29.99 S 36 16.00 O 876 8.00 N 808 7.00 C 3116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 161.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 108 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 238 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 54 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 56 " pdb="ZN ZN A 802 " - pdb=" SG CYS B 379 " pdb="ZN ZN A 802 " - pdb=" SG CYS B 382 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" NE2 HIS A 319 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 336 " pdb="ZN ZN A 804 " - pdb=" SG CYS B 55 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS A 55 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 319 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 336 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 108 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 238 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 54 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 56 " pdb="ZN ZN B 503 " - pdb=" SG CYS A 379 " pdb="ZN ZN B 503 " - pdb=" SG CYS A 382 " Number of angles added : 4 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 69.1% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 66 through 98 Processing helix chain 'A' and resid 100 through 126 Processing helix chain 'A' and resid 139 through 169 removed outlier: 4.344A pdb=" N THR A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 201 Processing helix chain 'A' and resid 231 through 259 Processing helix chain 'A' and resid 264 through 293 Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.619A pdb=" N CYS A 379 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 380 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG A 381 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 98 Processing helix chain 'B' and resid 100 through 126 Processing helix chain 'B' and resid 139 through 169 removed outlier: 4.347A pdb=" N THR B 143 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 201 Processing helix chain 'B' and resid 231 through 259 Processing helix chain 'B' and resid 264 through 293 Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.577A pdb=" N CYS B 379 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 325 removed outlier: 5.786A pdb=" N THR A 318 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA A 338 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU A 320 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 336 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS A 331 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR A 366 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 333 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN A 368 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 335 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU A 370 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 337 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 315 through 325 removed outlier: 5.723A pdb=" N THR B 318 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA B 338 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU B 320 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS B 336 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N HIS B 331 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR B 366 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 333 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLN B 368 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 335 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU B 370 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 337 " --> pdb=" O GLU B 370 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1516 1.34 - 1.46: 1161 1.46 - 1.58: 2227 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 4960 Sorted by residual: bond pdb=" CA HIS B 56 " pdb=" CB HIS B 56 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.30e-01 bond pdb=" CB HIS A 56 " pdb=" CG HIS A 56 " ideal model delta sigma weight residual 1.497 1.508 -0.011 1.40e-02 5.10e+03 5.69e-01 bond pdb=" CG PRO A 385 " pdb=" CD PRO A 385 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.42e-01 bond pdb=" CA HIS A 56 " pdb=" CB HIS A 56 " ideal model delta sigma weight residual 1.537 1.546 -0.010 1.31e-02 5.83e+03 5.36e-01 bond pdb=" CA ALA B 282 " pdb=" C ALA B 282 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.27e-01 ... (remaining 4955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 6569 1.18 - 2.37: 134 2.37 - 3.55: 43 3.55 - 4.73: 13 4.73 - 5.91: 5 Bond angle restraints: 6764 Sorted by residual: angle pdb=" CA HIS A 56 " pdb=" CB HIS A 56 " pdb=" CG HIS A 56 " ideal model delta sigma weight residual 113.80 115.95 -2.15 1.00e+00 1.00e+00 4.61e+00 angle pdb=" CB ILE B 275 " pdb=" CG1 ILE B 275 " pdb=" CD1 ILE B 275 " ideal model delta sigma weight residual 113.80 118.12 -4.32 2.10e+00 2.27e-01 4.24e+00 angle pdb=" CB ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CD1 ILE A 275 " ideal model delta sigma weight residual 113.80 118.09 -4.29 2.10e+00 2.27e-01 4.17e+00 angle pdb=" C CYS A 55 " pdb=" N HIS A 56 " pdb=" CA HIS A 56 " ideal model delta sigma weight residual 125.66 129.17 -3.51 1.85e+00 2.92e-01 3.61e+00 angle pdb=" C LEU A 169 " pdb=" CA LEU A 169 " pdb=" CB LEU A 169 " ideal model delta sigma weight residual 109.71 113.01 -3.30 1.83e+00 2.99e-01 3.25e+00 ... (remaining 6759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 2971 34.37 - 68.73: 113 68.73 - 103.10: 2 103.10 - 137.47: 0 137.47 - 171.84: 6 Dihedral angle restraints: 3092 sinusoidal: 1308 harmonic: 1784 Sorted by residual: dihedral pdb=" CA LEU A 169 " pdb=" C LEU A 169 " pdb=" N HIS A 170 " pdb=" CA HIS A 170 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N HIS B 170 " pdb=" CA HIS B 170 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CCH AV0 A 803 " pdb=" CCQ AV0 A 803 " pdb=" OCB AV0 A 803 " pdb=" CCS AV0 A 803 " ideal model delta sinusoidal sigma weight residual 127.39 -44.45 171.84 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 509 0.027 - 0.054: 193 0.054 - 0.081: 78 0.081 - 0.108: 30 0.108 - 0.135: 4 Chirality restraints: 814 Sorted by residual: chirality pdb=" CA HIS A 56 " pdb=" N HIS A 56 " pdb=" C HIS A 56 " pdb=" CB HIS A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL A 312 " pdb=" N VAL A 312 " pdb=" C VAL A 312 " pdb=" CB VAL A 312 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL B 312 " pdb=" N VAL B 312 " pdb=" C VAL B 312 " pdb=" CB VAL B 312 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 811 not shown) Planarity restraints: 826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 384 " -0.028 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 385 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 384 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A 385 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 296 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.79e-01 pdb=" N PRO B 297 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " -0.014 5.00e-02 4.00e+02 ... (remaining 823 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 20 2.33 - 2.98: 2468 2.98 - 3.62: 7381 3.62 - 4.26: 10754 4.26 - 4.90: 18353 Nonbonded interactions: 38976 Sorted by model distance: nonbonded pdb=" SG CYS A 55 " pdb=" OE2 GLU B 370 " model vdw 1.693 3.400 nonbonded pdb=" OD2 ASP B 242 " pdb="ZN ZN B 502 " model vdw 1.965 2.230 nonbonded pdb=" OD2 ASP A 242 " pdb="ZN ZN A 801 " model vdw 1.966 2.230 nonbonded pdb=" OE2 GLU A 370 " pdb="ZN ZN A 804 " model vdw 1.970 2.230 nonbonded pdb=" OE2 GLU B 370 " pdb="ZN ZN B 501 " model vdw 1.982 2.230 ... (remaining 38971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 54 through 802) selection = (chain 'B' and resid 54 through 502) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4978 Z= 0.147 Angle : 0.503 7.480 6768 Z= 0.239 Chirality : 0.036 0.135 814 Planarity : 0.004 0.044 826 Dihedral : 19.008 171.837 1936 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.60 % Allowed : 24.20 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.37 (0.35), residues: 606 helix: 4.30 (0.21), residues: 394 sheet: -0.10 (0.82), residues: 52 loop : 0.11 (0.59), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 167 TYR 0.006 0.001 TYR A 372 PHE 0.007 0.001 PHE A 302 TRP 0.006 0.001 TRP A 324 HIS 0.004 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4960) covalent geometry : angle 0.49495 ( 6764) hydrogen bonds : bond 0.10912 ( 350) hydrogen bonds : angle 4.51629 ( 1038) metal coordination : bond 0.00685 ( 18) metal coordination : angle 3.78518 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.191 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.3919 time to fit residues: 31.8777 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 80 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.071408 restraints weight = 7447.119| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.36 r_work: 0.2742 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4978 Z= 0.182 Angle : 0.531 7.675 6768 Z= 0.250 Chirality : 0.037 0.131 814 Planarity : 0.004 0.041 826 Dihedral : 16.420 174.370 917 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.60 % Allowed : 22.60 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.27 (0.35), residues: 606 helix: 4.25 (0.22), residues: 402 sheet: -0.25 (0.84), residues: 48 loop : -0.24 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.005 0.001 TYR A 330 PHE 0.007 0.001 PHE A 165 TRP 0.011 0.001 TRP A 324 HIS 0.006 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4960) covalent geometry : angle 0.51986 ( 6764) hydrogen bonds : bond 0.04683 ( 350) hydrogen bonds : angle 3.81058 ( 1038) metal coordination : bond 0.00901 ( 18) metal coordination : angle 4.43996 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.208 Fit side-chains REVERT: A 303 GLU cc_start: 0.8039 (mp0) cc_final: 0.7826 (mp0) REVERT: A 344 ASP cc_start: 0.8745 (t0) cc_final: 0.8449 (t0) REVERT: B 344 ASP cc_start: 0.8758 (t0) cc_final: 0.8466 (t0) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.3657 time to fit residues: 28.1922 Evaluate side-chains 73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.072178 restraints weight = 7382.874| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.34 r_work: 0.2763 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4978 Z= 0.122 Angle : 0.505 9.699 6768 Z= 0.229 Chirality : 0.035 0.130 814 Planarity : 0.004 0.040 826 Dihedral : 16.252 174.059 917 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.60 % Allowed : 21.60 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.26 (0.35), residues: 606 helix: 4.28 (0.22), residues: 404 sheet: -0.26 (0.83), residues: 48 loop : -0.47 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.005 0.001 TYR A 372 PHE 0.007 0.001 PHE B 165 TRP 0.009 0.001 TRP A 324 HIS 0.007 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4960) covalent geometry : angle 0.48663 ( 6764) hydrogen bonds : bond 0.04242 ( 350) hydrogen bonds : angle 3.58563 ( 1038) metal coordination : bond 0.00819 ( 18) metal coordination : angle 5.58277 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.182 Fit side-chains REVERT: A 344 ASP cc_start: 0.8775 (t0) cc_final: 0.8354 (t0) REVERT: B 344 ASP cc_start: 0.8784 (t0) cc_final: 0.8365 (t0) outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 0.3762 time to fit residues: 31.9488 Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 0.0050 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.072576 restraints weight = 7409.699| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.35 r_work: 0.2778 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4978 Z= 0.107 Angle : 0.509 10.639 6768 Z= 0.228 Chirality : 0.035 0.125 814 Planarity : 0.004 0.039 826 Dihedral : 16.090 172.955 915 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.20 % Allowed : 21.00 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.31 (0.35), residues: 606 helix: 4.34 (0.22), residues: 404 sheet: -0.24 (0.83), residues: 48 loop : -0.49 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 132 TYR 0.005 0.001 TYR A 372 PHE 0.009 0.001 PHE A 165 TRP 0.008 0.001 TRP B 324 HIS 0.011 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 4960) covalent geometry : angle 0.49458 ( 6764) hydrogen bonds : bond 0.03977 ( 350) hydrogen bonds : angle 3.47423 ( 1038) metal coordination : bond 0.00701 ( 18) metal coordination : angle 4.94849 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.257 Fit side-chains REVERT: A 344 ASP cc_start: 0.8828 (t0) cc_final: 0.8389 (t0) REVERT: B 344 ASP cc_start: 0.8833 (t0) cc_final: 0.8395 (t0) REVERT: B 373 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8169 (mm-40) outliers start: 6 outliers final: 1 residues processed: 83 average time/residue: 0.3662 time to fit residues: 32.3617 Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 373 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.072787 restraints weight = 7439.816| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.32 r_work: 0.2777 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4978 Z= 0.115 Angle : 0.515 10.696 6768 Z= 0.231 Chirality : 0.035 0.124 814 Planarity : 0.004 0.039 826 Dihedral : 16.015 172.513 914 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 21.80 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.30 (0.35), residues: 606 helix: 4.33 (0.22), residues: 404 sheet: -0.17 (0.85), residues: 48 loop : -0.51 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 132 TYR 0.004 0.001 TYR A 372 PHE 0.005 0.001 PHE B 165 TRP 0.008 0.001 TRP A 324 HIS 0.010 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4960) covalent geometry : angle 0.50275 ( 6764) hydrogen bonds : bond 0.03944 ( 350) hydrogen bonds : angle 3.43561 ( 1038) metal coordination : bond 0.00617 ( 18) metal coordination : angle 4.63140 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.116 Fit side-chains REVERT: A 344 ASP cc_start: 0.8844 (t0) cc_final: 0.8418 (t0) REVERT: B 344 ASP cc_start: 0.8857 (t0) cc_final: 0.8430 (t0) REVERT: B 373 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8173 (mm-40) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 0.3091 time to fit residues: 28.1314 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 373 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072282 restraints weight = 7596.037| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.37 r_work: 0.2775 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4978 Z= 0.121 Angle : 0.518 10.843 6768 Z= 0.233 Chirality : 0.035 0.124 814 Planarity : 0.004 0.038 826 Dihedral : 15.988 172.139 914 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.40 % Allowed : 22.40 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.35), residues: 606 helix: 4.30 (0.22), residues: 404 sheet: -0.17 (0.85), residues: 48 loop : -0.50 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.005 0.001 TYR A 372 PHE 0.009 0.001 PHE B 165 TRP 0.007 0.001 TRP B 324 HIS 0.010 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4960) covalent geometry : angle 0.50629 ( 6764) hydrogen bonds : bond 0.03975 ( 350) hydrogen bonds : angle 3.42400 ( 1038) metal coordination : bond 0.00637 ( 18) metal coordination : angle 4.54162 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.183 Fit side-chains REVERT: A 344 ASP cc_start: 0.8867 (t0) cc_final: 0.8454 (t0) REVERT: B 344 ASP cc_start: 0.8868 (t0) cc_final: 0.8455 (t0) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.3596 time to fit residues: 31.7361 Evaluate side-chains 81 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.072078 restraints weight = 7421.510| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.33 r_work: 0.2785 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4978 Z= 0.136 Angle : 0.529 11.454 6768 Z= 0.237 Chirality : 0.035 0.123 814 Planarity : 0.004 0.038 826 Dihedral : 15.984 172.070 914 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.40 % Allowed : 22.40 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.24 (0.35), residues: 606 helix: 4.26 (0.22), residues: 404 sheet: -0.19 (0.86), residues: 48 loop : -0.48 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.005 0.001 TYR A 372 PHE 0.005 0.001 PHE A 302 TRP 0.008 0.001 TRP B 324 HIS 0.010 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4960) covalent geometry : angle 0.51824 ( 6764) hydrogen bonds : bond 0.04070 ( 350) hydrogen bonds : angle 3.43570 ( 1038) metal coordination : bond 0.00619 ( 18) metal coordination : angle 4.38025 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.209 Fit side-chains REVERT: A 344 ASP cc_start: 0.8854 (t0) cc_final: 0.8433 (t0) REVERT: B 344 ASP cc_start: 0.8856 (t0) cc_final: 0.8434 (t0) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.3403 time to fit residues: 28.6790 Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.072574 restraints weight = 7463.075| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.34 r_work: 0.2789 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4978 Z= 0.117 Angle : 0.525 11.912 6768 Z= 0.233 Chirality : 0.035 0.124 814 Planarity : 0.004 0.038 826 Dihedral : 15.935 171.583 914 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.80 % Allowed : 21.80 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.23 (0.35), residues: 606 helix: 4.26 (0.22), residues: 404 sheet: -0.20 (0.85), residues: 48 loop : -0.52 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.006 0.001 TYR B 77 PHE 0.007 0.001 PHE A 165 TRP 0.008 0.001 TRP B 324 HIS 0.010 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4960) covalent geometry : angle 0.51349 ( 6764) hydrogen bonds : bond 0.03956 ( 350) hydrogen bonds : angle 3.38664 ( 1038) metal coordination : bond 0.00673 ( 18) metal coordination : angle 4.45164 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.185 Fit side-chains REVERT: A 344 ASP cc_start: 0.8854 (t0) cc_final: 0.8435 (t0) REVERT: B 344 ASP cc_start: 0.8857 (t0) cc_final: 0.8436 (t0) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.3081 time to fit residues: 27.3693 Evaluate side-chains 83 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.072869 restraints weight = 7361.377| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.31 r_work: 0.2778 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4978 Z= 0.117 Angle : 0.526 12.005 6768 Z= 0.234 Chirality : 0.035 0.124 814 Planarity : 0.004 0.037 826 Dihedral : 15.901 171.368 914 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.80 % Allowed : 22.20 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.23 (0.34), residues: 606 helix: 4.27 (0.22), residues: 404 sheet: -0.21 (0.85), residues: 48 loop : -0.52 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.006 0.001 TYR B 77 PHE 0.004 0.001 PHE A 258 TRP 0.008 0.001 TRP B 324 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4960) covalent geometry : angle 0.51582 ( 6764) hydrogen bonds : bond 0.03935 ( 350) hydrogen bonds : angle 3.35207 ( 1038) metal coordination : bond 0.00628 ( 18) metal coordination : angle 4.23455 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.177 Fit side-chains REVERT: A 344 ASP cc_start: 0.8886 (t0) cc_final: 0.8474 (t0) REVERT: B 344 ASP cc_start: 0.8883 (t0) cc_final: 0.8470 (t0) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.3381 time to fit residues: 29.9258 Evaluate side-chains 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.0030 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072196 restraints weight = 7340.216| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.32 r_work: 0.2768 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4978 Z= 0.141 Angle : 0.538 12.078 6768 Z= 0.242 Chirality : 0.036 0.123 814 Planarity : 0.004 0.038 826 Dihedral : 15.920 171.433 914 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.60 % Allowed : 22.80 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.19 (0.35), residues: 606 helix: 4.22 (0.22), residues: 404 sheet: -0.22 (0.85), residues: 48 loop : -0.49 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.007 0.001 TYR A 77 PHE 0.007 0.001 PHE B 165 TRP 0.008 0.001 TRP B 324 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4960) covalent geometry : angle 0.53126 ( 6764) hydrogen bonds : bond 0.04090 ( 350) hydrogen bonds : angle 3.39038 ( 1038) metal coordination : bond 0.00520 ( 18) metal coordination : angle 3.45450 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.192 Fit side-chains REVERT: A 344 ASP cc_start: 0.8899 (t0) cc_final: 0.8513 (t0) REVERT: B 344 ASP cc_start: 0.8898 (t0) cc_final: 0.8478 (t0) outliers start: 8 outliers final: 8 residues processed: 79 average time/residue: 0.3184 time to fit residues: 26.8904 Evaluate side-chains 79 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 57 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072774 restraints weight = 7401.310| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.33 r_work: 0.2797 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4978 Z= 0.112 Angle : 0.528 12.392 6768 Z= 0.235 Chirality : 0.035 0.126 814 Planarity : 0.004 0.037 826 Dihedral : 15.844 170.793 914 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.80 % Allowed : 22.60 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.22 (0.34), residues: 606 helix: 4.27 (0.22), residues: 404 sheet: -0.19 (0.84), residues: 48 loop : -0.56 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.007 0.001 TYR B 77 PHE 0.003 0.001 PHE A 302 TRP 0.008 0.001 TRP B 324 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4960) covalent geometry : angle 0.51955 ( 6764) hydrogen bonds : bond 0.03899 ( 350) hydrogen bonds : angle 3.33254 ( 1038) metal coordination : bond 0.00569 ( 18) metal coordination : angle 3.83114 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1530.62 seconds wall clock time: 26 minutes 53.88 seconds (1613.88 seconds total)