Starting phenix.real_space_refine on Wed Sep 17 11:03:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7y_44328/09_2025/9b7y_44328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7y_44328/09_2025/9b7y_44328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7y_44328/09_2025/9b7y_44328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7y_44328/09_2025/9b7y_44328.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7y_44328/09_2025/9b7y_44328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7y_44328/09_2025/9b7y_44328.cif" } resolution = 2.51 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= 0.015 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 P 120 5.49 5 S 12 5.16 5 C 4863 2.51 5 N 1562 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8361 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2954 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2947 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 640 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 599 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Time building chain proxies: 2.02, per 1000 atoms: 0.24 Number of scatterers: 8361 At special positions: 0 Unit cell: (155.8, 99.75, 92.15, 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 12 16.00 P 120 15.00 O 1804 8.00 N 1562 7.00 C 4863 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: 0.69 Conformation dependent library (CDL) restraints added in 334.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 85.3% alpha, 0.0% beta 46 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 Processing helix chain 'A' and resid 36 through 44 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.575A pdb=" N LEU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 78 Processing helix chain 'A' and resid 90 through 105 removed outlier: 4.836A pdb=" N GLU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.060A pdb=" N TRP A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 120 through 146 Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.683A pdb=" N HIS A 171 " --> pdb=" O LEU A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 234 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 261 through 288 removed outlier: 3.511A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 309 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 324 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.795A pdb=" N ARG A 380 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.741A pdb=" N GLU A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'D' and resid 14 through 30 Processing helix chain 'D' and resid 36 through 44 Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.815A pdb=" N LEU D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 78 Processing helix chain 'D' and resid 90 through 105 removed outlier: 5.172A pdb=" N GLU D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.694A pdb=" N THR D 109 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 120 through 146 Processing helix chain 'D' and resid 150 through 169 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.875A pdb=" N VAL D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.625A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 261 through 288 removed outlier: 4.013A pdb=" N ILE D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 Processing helix chain 'D' and resid 309 through 319 Processing helix chain 'D' and resid 320 through 323 Processing helix chain 'D' and resid 324 through 350 Processing helix chain 'D' and resid 354 through 375 Processing helix chain 'D' and resid 376 through 380 removed outlier: 3.786A pdb=" N ARG D 380 " --> pdb=" O HIS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 398 removed outlier: 3.747A pdb=" N GLU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1166 1.32 - 1.44: 2839 1.44 - 1.56: 4492 1.56 - 1.69: 236 1.69 - 1.81: 16 Bond restraints: 8749 Sorted by residual: bond pdb=" C LEU A 95 " pdb=" O LEU A 95 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" C ALA A 102 " pdb=" O ALA A 102 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" N ARG A 89 " pdb=" CA ARG A 89 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.23e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.46e-02 4.69e+03 5.67e+00 bond pdb=" N ASP A 211 " pdb=" CA ASP A 211 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.63e+00 ... (remaining 8744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 12061 1.78 - 3.56: 287 3.56 - 5.34: 17 5.34 - 7.12: 4 7.12 - 8.89: 2 Bond angle restraints: 12371 Sorted by residual: angle pdb=" N GLN A 113 " pdb=" CA GLN A 113 " pdb=" C GLN A 113 " ideal model delta sigma weight residual 111.36 118.55 -7.19 1.09e+00 8.42e-01 4.35e+01 angle pdb=" N ALA D 48 " pdb=" CA ALA D 48 " pdb=" C ALA D 48 " ideal model delta sigma weight residual 111.33 118.33 -7.00 1.21e+00 6.83e-01 3.35e+01 angle pdb=" N ARG D 106 " pdb=" CA ARG D 106 " pdb=" C ARG D 106 " ideal model delta sigma weight residual 111.28 116.98 -5.70 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N LEU A 108 " pdb=" CA LEU A 108 " pdb=" C LEU A 108 " ideal model delta sigma weight residual 113.19 118.60 -5.41 1.19e+00 7.06e-01 2.07e+01 angle pdb=" N ARG A 106 " pdb=" CA ARG A 106 " pdb=" C ARG A 106 " ideal model delta sigma weight residual 111.28 116.05 -4.77 1.09e+00 8.42e-01 1.91e+01 ... (remaining 12366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 4343 34.84 - 69.67: 611 69.67 - 104.51: 10 104.51 - 139.34: 2 139.34 - 174.18: 3 Dihedral angle restraints: 4969 sinusoidal: 2741 harmonic: 2228 Sorted by residual: dihedral pdb=" C4' DG F 33 " pdb=" C3' DG F 33 " pdb=" O3' DG F 33 " pdb=" P DC F 34 " ideal model delta sinusoidal sigma weight residual 220.00 45.82 174.18 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC C 10 " pdb=" C3' DC C 10 " pdb=" O3' DC C 10 " pdb=" P DC C 11 " ideal model delta sinusoidal sigma weight residual 220.00 49.27 170.73 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG F 35 " pdb=" C3' DG F 35 " pdb=" O3' DG F 35 " pdb=" P DA F 36 " ideal model delta sinusoidal sigma weight residual 220.00 73.23 146.77 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1302 0.066 - 0.132: 105 0.132 - 0.198: 7 0.198 - 0.264: 5 0.264 - 0.330: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA TRP A 112 " pdb=" N TRP A 112 " pdb=" C TRP A 112 " pdb=" CB TRP A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C3' DC C 10 " pdb=" C4' DC C 10 " pdb=" O3' DC C 10 " pdb=" C2' DC C 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' DG F 33 " pdb=" C4' DG F 33 " pdb=" O3' DG F 33 " pdb=" C2' DG F 33 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1419 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 252 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 253 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 89 " -0.196 9.50e-02 1.11e+02 8.78e-02 4.73e+00 pdb=" NE ARG A 89 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 89 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 89 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 89 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 107 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C ALA A 107 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 107 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 108 " -0.010 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2558 2.85 - 3.36: 7612 3.36 - 3.87: 15605 3.87 - 4.39: 17403 4.39 - 4.90: 26826 Nonbonded interactions: 70004 Sorted by model distance: nonbonded pdb=" N4 DC B 106 " pdb=" O6 DG C 18 " model vdw 2.333 3.120 nonbonded pdb=" N6 DA B 110 " pdb=" O4 DT C 14 " model vdw 2.337 3.120 nonbonded pdb=" OE1 GLN A 335 " pdb=" NH2 ARG A 338 " model vdw 2.348 3.120 nonbonded pdb=" N GLU D 178 " pdb=" OE1 GLU D 178 " model vdw 2.351 3.120 nonbonded pdb=" O4 DT B 96 " pdb=" N6 DA C 28 " model vdw 2.377 3.120 ... (remaining 69999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 211 or (resid 212 throu \ gh 213 and (name N or name CA or name C or name O or name CB )) or resid 214 thr \ ough 401)) selection = (chain 'D' and (resid 8 through 209 or (resid 210 and (name N or name CA or name \ C or name O or name CB )) or resid 211 through 401)) } ncs_group { reference = chain 'B' selection = (chain 'E' and resid 86 through 114) } ncs_group { reference = chain 'C' selection = (chain 'F' and resid 10 through 38) } 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: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.460 Find NCS groups from input model: 0.100 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 0.041 8749 Z= 0.235 Angle : 0.580 8.895 12371 Z= 0.378 Chirality : 0.041 0.330 1422 Planarity : 0.005 0.088 1180 Dihedral : 24.660 174.178 3525 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % 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: 3.53 (0.31), residues: 758 helix: 2.87 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.16 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 106 TYR 0.008 0.001 TYR A 256 PHE 0.009 0.001 PHE D 32 TRP 0.014 0.001 TRP A 112 HIS 0.001 0.000 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8749) covalent geometry : angle 0.58031 (12371) hydrogen bonds : bond 0.12857 ( 575) hydrogen bonds : angle 3.98677 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7764 (ttm110) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.0117 time to fit residues: 43.0737 Evaluate side-chains 35 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086992 restraints weight = 11377.771| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.57 r_work: 0.3020 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8749 Z= 0.179 Angle : 0.513 6.533 12371 Z= 0.293 Chirality : 0.033 0.127 1422 Planarity : 0.004 0.056 1180 Dihedral : 27.357 176.532 2162 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.00 % Allowed : 14.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.61 (0.31), residues: 758 helix: 2.93 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.08 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 128 TYR 0.017 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.013 0.001 TRP A 112 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8749) covalent geometry : angle 0.51261 (12371) hydrogen bonds : bond 0.05536 ( 575) hydrogen bonds : angle 3.53620 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8323 (ttt180) cc_final: 0.7959 (ttp-110) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.9804 time to fit residues: 42.8628 Evaluate side-chains 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 23 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.116532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087125 restraints weight = 11214.568| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.56 r_work: 0.3023 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8749 Z= 0.161 Angle : 0.495 6.236 12371 Z= 0.284 Chirality : 0.032 0.124 1422 Planarity : 0.004 0.055 1180 Dihedral : 27.351 175.445 2162 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.00 % Allowed : 14.38 % Favored : 84.62 % 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: 3.69 (0.31), residues: 758 helix: 3.04 (0.21), residues: 596 sheet: None (None), residues: 0 loop : 0.05 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 128 TYR 0.015 0.002 TYR A 256 PHE 0.009 0.001 PHE D 32 TRP 0.015 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8749) covalent geometry : angle 0.49456 (12371) hydrogen bonds : bond 0.05088 ( 575) hydrogen bonds : angle 3.45120 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 294 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8632 (ttm170) REVERT: A 304 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7950 (ttm110) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.8965 time to fit residues: 40.1789 Evaluate side-chains 43 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.114934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085328 restraints weight = 11440.268| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.58 r_work: 0.2992 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.191 Angle : 0.514 6.181 12371 Z= 0.294 Chirality : 0.034 0.124 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.366 176.094 2162 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.17 % Allowed : 14.55 % Favored : 84.28 % 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: 3.62 (0.31), residues: 758 helix: 2.95 (0.21), residues: 602 sheet: None (None), residues: 0 loop : 0.08 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.016 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.013 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8749) covalent geometry : angle 0.51368 (12371) hydrogen bonds : bond 0.05614 ( 575) hydrogen bonds : angle 3.52813 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8655 (ttm170) REVERT: A 304 ARG cc_start: 0.8357 (ttt180) cc_final: 0.7978 (ttm110) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.9362 time to fit residues: 40.9870 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084868 restraints weight = 11241.837| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.56 r_work: 0.2983 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8749 Z= 0.199 Angle : 0.523 6.861 12371 Z= 0.299 Chirality : 0.034 0.123 1422 Planarity : 0.004 0.054 1180 Dihedral : 27.374 176.867 2162 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.67 % Allowed : 14.38 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.60 (0.31), residues: 758 helix: 2.98 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.05 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.015 0.002 TYR A 256 PHE 0.011 0.001 PHE D 32 TRP 0.012 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8749) covalent geometry : angle 0.52278 (12371) hydrogen bonds : bond 0.05739 ( 575) hydrogen bonds : angle 3.56514 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.274 Fit side-chains REVERT: A 89 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8310 (ptm160) REVERT: A 214 ASP cc_start: 0.8252 (m-30) cc_final: 0.7788 (p0) REVERT: A 294 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8668 (ttm170) REVERT: D 178 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7399 (mm-30) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 0.8776 time to fit residues: 38.4095 Evaluate side-chains 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.0030 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086481 restraints weight = 11171.759| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.55 r_work: 0.3009 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8749 Z= 0.160 Angle : 0.494 7.065 12371 Z= 0.284 Chirality : 0.032 0.125 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.312 176.595 2162 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.51 % Allowed : 14.88 % Favored : 83.61 % 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: 3.67 (0.31), residues: 758 helix: 3.03 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.06 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 277 TYR 0.015 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.012 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8749) covalent geometry : angle 0.49396 (12371) hydrogen bonds : bond 0.05082 ( 575) hydrogen bonds : angle 3.45603 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.262 Fit side-chains REVERT: A 294 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8606 (ttm170) REVERT: D 178 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7357 (mm-30) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.9321 time to fit residues: 42.7824 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085687 restraints weight = 11406.732| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.57 r_work: 0.2994 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.179 Angle : 0.504 6.872 12371 Z= 0.290 Chirality : 0.033 0.122 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.285 176.599 2162 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 14.21 % Favored : 84.11 % 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: 3.67 (0.31), residues: 758 helix: 3.06 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.04 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.014 0.002 TYR A 256 PHE 0.011 0.001 PHE D 32 TRP 0.011 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8749) covalent geometry : angle 0.50375 (12371) hydrogen bonds : bond 0.05391 ( 575) hydrogen bonds : angle 3.49315 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.254 Fit side-chains REVERT: A 294 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8665 (ttm170) REVERT: D 178 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7373 (mm-30) outliers start: 10 outliers final: 8 residues processed: 41 average time/residue: 0.8880 time to fit residues: 38.0773 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085920 restraints weight = 11318.096| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.56 r_work: 0.3000 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.172 Angle : 0.503 7.294 12371 Z= 0.288 Chirality : 0.033 0.122 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.283 176.615 2162 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.51 % Allowed : 14.55 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.68 (0.31), residues: 758 helix: 3.07 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.015 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.011 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8749) covalent geometry : angle 0.50254 (12371) hydrogen bonds : bond 0.05324 ( 575) hydrogen bonds : angle 3.48857 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.266 Fit side-chains REVERT: A 294 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8653 (ttm170) REVERT: D 178 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7359 (mm-30) outliers start: 9 outliers final: 8 residues processed: 41 average time/residue: 0.8973 time to fit residues: 38.4581 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086223 restraints weight = 11274.173| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.56 r_work: 0.3006 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.163 Angle : 0.498 7.365 12371 Z= 0.286 Chirality : 0.032 0.123 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.275 176.577 2162 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.51 % Allowed : 14.55 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.70 (0.31), residues: 758 helix: 3.08 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.016 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.011 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8749) covalent geometry : angle 0.49778 (12371) hydrogen bonds : bond 0.05186 ( 575) hydrogen bonds : angle 3.46628 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.258 Fit side-chains REVERT: A 294 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8635 (ttm170) REVERT: D 178 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7362 (mm-30) outliers start: 9 outliers final: 7 residues processed: 40 average time/residue: 0.9501 time to fit residues: 39.6512 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085243 restraints weight = 11238.128| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.57 r_work: 0.2988 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.187 Angle : 0.513 7.315 12371 Z= 0.294 Chirality : 0.034 0.120 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.282 176.963 2162 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.84 % Allowed : 14.38 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.56 (0.31), residues: 758 helix: 2.95 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.11 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 157 TYR 0.015 0.002 TYR A 256 PHE 0.011 0.001 PHE D 32 TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8749) covalent geometry : angle 0.51268 (12371) hydrogen bonds : bond 0.05579 ( 575) hydrogen bonds : angle 3.53186 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.249 Fit side-chains REVERT: A 89 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8268 (ptm160) REVERT: A 294 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8669 (ttm170) REVERT: D 178 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7429 (mm-30) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.9756 time to fit residues: 43.6169 Evaluate side-chains 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086073 restraints weight = 11252.856| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.56 r_work: 0.3003 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8749 Z= 0.162 Angle : 0.500 7.359 12371 Z= 0.287 Chirality : 0.032 0.121 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.279 176.927 2162 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.51 % Allowed : 14.72 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.68 (0.31), residues: 758 helix: 3.06 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.04 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 9 TYR 0.016 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.011 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8749) covalent geometry : angle 0.49960 (12371) hydrogen bonds : bond 0.05227 ( 575) hydrogen bonds : angle 3.48491 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.55 seconds wall clock time: 57 minutes 36.56 seconds (3456.56 seconds total)