Starting phenix.real_space_refine on Thu Jul 2 10:08:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7y_44328/07_2026/9b7y_44328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7y_44328/07_2026/9b7y_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b7y_44328/07_2026/9b7y_44328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7y_44328/07_2026/9b7y_44328.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7y_44328/07_2026/9b7y_44328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7y_44328/07_2026/9b7y_44328.map" } 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-dev-6108/lib/python3.11/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: 2.13, per 1000 atoms: 0.25 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: 0.75 Conformation dependent library (CDL) restraints added in 408.8 milliseconds 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: 1.12 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: 1.55 Time building geometry restraints manager: 1.04 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=" C3' DA F 29 " pdb=" C2' DA F 29 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DC F 21 " pdb=" C2' DC F 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 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=" C3' DC C 20 " pdb=" C2' DC C 20 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG C 35 " pdb=" C2' DG C 35 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 8744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 11888 1.78 - 3.56: 458 3.56 - 5.34: 18 5.34 - 7.12: 5 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 - 0.071: 1257 0.071 - 0.141: 151 0.141 - 0.212: 4 0.212 - 0.283: 7 0.283 - 0.354: 3 Chirality restraints: 1422 Sorted by residual: 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 -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.13e+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 -2.73 -2.38 -0.35 2.00e-01 2.50e+01 2.99e+00 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 ... (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: 8.030 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 10.030 Find NCS groups from input model: 0.120 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.005 0.041 8749 Z= 0.425 Angle : 0.679 8.895 12371 Z= 0.562 Chirality : 0.048 0.354 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 are 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/Z covalent geometry : bond 0.00499 / 0.43 ( 8749) covalent geometry : angle 0.67859 / 0.56 (12371) hydrogen bonds : bond 0.12857 / 8.23 ( 575) hydrogen bonds : angle 3.98677 / 2.93 ( 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 : 0.277 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: 1.0379 time to fit residues: 44.2763 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 : 0.266 ------------------------------------------------------------------------------- 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... A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.116896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087536 restraints weight = 11365.851| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.59 r_work: 0.3029 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8749 Z= 0.163 Angle : 0.539 6.204 12371 Z= 0.317 Chirality : 0.038 0.219 1422 Planarity : 0.004 0.059 1180 Dihedral : 27.573 179.773 2162 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.00 % Allowed : 14.21 % Favored : 84.78 % 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 are not related in a simple way. whole: 3.57 (0.31), residues: 758 helix: 2.89 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.08 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 128 TYR 0.018 0.002 TYR A 256 PHE 0.011 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/Z covalent geometry : bond 0.00321 / 0.16 ( 8749) covalent geometry : angle 0.53945 / 0.32 (12371) hydrogen bonds : bond 0.05748 / 3.89 ( 575) hydrogen bonds : angle 3.57793 / 2.65 ( 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 89 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (ptm-80) REVERT: A 304 ARG cc_start: 0.8278 (ttt180) cc_final: 0.7903 (ttm110) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 1.0479 time to fit residues: 45.8497 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 197 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: 4.9990 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086951 restraints weight = 11194.390| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.56 r_work: 0.3020 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8749 Z= 0.153 Angle : 0.519 6.680 12371 Z= 0.304 Chirality : 0.037 0.252 1422 Planarity : 0.004 0.055 1180 Dihedral : 27.671 177.517 2162 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.00 % Allowed : 14.88 % 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 are not related in a simple way. whole: 3.63 (0.31), residues: 758 helix: 2.94 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.07 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 114 TYR 0.017 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.014 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 8749) covalent geometry : angle 0.51898 / 0.30 (12371) hydrogen bonds : bond 0.05590 / 3.82 ( 575) hydrogen bonds : angle 3.52508 / 2.61 ( 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 45 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8327 (ttt180) cc_final: 0.7991 (ttp-110) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.9849 time to fit residues: 43.1074 Evaluate side-chains 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU 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: 0.5980 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084473 restraints weight = 11430.269| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.57 r_work: 0.2974 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8749 Z= 0.211 Angle : 0.569 6.898 12371 Z= 0.326 Chirality : 0.040 0.259 1422 Planarity : 0.004 0.054 1180 Dihedral : 27.752 177.879 2162 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.84 % Allowed : 14.55 % 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 are not related in a simple way. whole: 3.50 (0.31), residues: 758 helix: 2.85 (0.21), residues: 602 sheet: None (None), residues: 0 loop : 0.06 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 114 TYR 0.016 0.002 TYR A 256 PHE 0.012 0.002 PHE D 32 TRP 0.013 0.002 TRP A 112 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 ( 8749) covalent geometry : angle 0.56856 / 0.33 (12371) hydrogen bonds : bond 0.06471 / 4.43 ( 575) hydrogen bonds : angle 3.67018 / 2.73 ( 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 39 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 89 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8359 (ptm-80) REVERT: A 304 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7988 (ttm110) REVERT: D 181 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8050 (tttp) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 1.1103 time to fit residues: 43.8615 Evaluate side-chains 38 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain D residue 35 VAL 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: 0.8980 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085184 restraints weight = 11250.431| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.55 r_work: 0.2988 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8749 Z= 0.172 Angle : 0.538 6.095 12371 Z= 0.312 Chirality : 0.038 0.260 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.764 177.633 2162 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.67 % Allowed : 13.88 % Favored : 84.45 % 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 are not related in a simple way. whole: 3.47 (0.31), residues: 758 helix: 2.85 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.01 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 338 TYR 0.018 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.013 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 8749) covalent geometry : angle 0.53762 / 0.31 (12371) hydrogen bonds : bond 0.05952 / 4.08 ( 575) hydrogen bonds : angle 3.61101 / 2.68 ( 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 47 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8354 (ttt180) cc_final: 0.7984 (ttm110) REVERT: D 181 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8053 (tttm) outliers start: 10 outliers final: 6 residues processed: 43 average time/residue: 0.9472 time to fit residues: 42.5790 Evaluate side-chains 42 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086000 restraints weight = 11147.925| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.54 r_work: 0.2999 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8749 Z= 0.153 Angle : 0.526 7.307 12371 Z= 0.305 Chirality : 0.037 0.259 1422 Planarity : 0.004 0.054 1180 Dihedral : 27.766 177.762 2162 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.17 % Allowed : 14.21 % 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 are not related in a simple way. whole: 3.62 (0.31), residues: 758 helix: 2.99 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.04 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.017 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/Z covalent geometry : bond 0.00300 / 0.15 ( 8749) covalent geometry : angle 0.52638 / 0.31 (12371) hydrogen bonds : bond 0.05580 / 3.82 ( 575) hydrogen bonds : angle 3.53800 / 2.62 ( 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 45 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 89 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8272 (ptm160) REVERT: A 304 ARG cc_start: 0.8315 (ttt180) cc_final: 0.7933 (ttm110) REVERT: D 181 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7994 (tttm) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.9556 time to fit residues: 42.8934 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 : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 6.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085105 restraints weight = 11367.985| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.57 r_work: 0.2987 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8749 Z= 0.171 Angle : 0.546 7.344 12371 Z= 0.313 Chirality : 0.038 0.264 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.810 177.130 2162 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.67 % Allowed : 13.71 % 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 are not related in a simple way. whole: 3.52 (0.31), residues: 758 helix: 2.88 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.00 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 333 TYR 0.015 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/Z covalent geometry : bond 0.00351 / 0.17 ( 8749) covalent geometry : angle 0.54551 / 0.31 (12371) hydrogen bonds : bond 0.05928 / 4.06 ( 575) hydrogen bonds : angle 3.60021 / 2.67 ( 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 46 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.276 Fit side-chains REVERT: A 89 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8307 (ptm160) REVERT: A 214 ASP cc_start: 0.8287 (m-30) cc_final: 0.7789 (p0) REVERT: D 181 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7999 (tttm) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.9109 time to fit residues: 40.9851 Evaluate side-chains 44 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085792 restraints weight = 11265.635| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.56 r_work: 0.2999 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8749 Z= 0.142 Angle : 0.526 7.484 12371 Z= 0.303 Chirality : 0.037 0.261 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.806 177.070 2162 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.51 % Allowed : 14.21 % 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 are not related in a simple way. whole: 3.65 (0.31), residues: 758 helix: 3.01 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 210 TYR 0.017 0.002 TYR A 256 PHE 0.011 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/Z covalent geometry : bond 0.00264 / 0.14 ( 8749) covalent geometry : angle 0.52614 / 0.30 (12371) hydrogen bonds : bond 0.05598 / 3.84 ( 575) hydrogen bonds : angle 3.55072 / 2.63 ( 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 : 0.286 Fit side-chains REVERT: A 89 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8301 (ptm160) REVERT: D 181 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7984 (tttm) outliers start: 9 outliers final: 8 residues processed: 40 average time/residue: 0.9483 time to fit residues: 39.6781 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 : 0.281 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086302 restraints weight = 11257.739| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.55 r_work: 0.3009 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8749 Z= 0.147 Angle : 0.520 8.034 12371 Z= 0.300 Chirality : 0.037 0.263 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.783 176.824 2162 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.34 % Allowed : 14.72 % 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 are not related in a simple way. whole: 3.68 (0.31), residues: 758 helix: 3.03 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.09 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 124 TYR 0.015 0.002 TYR A 256 PHE 0.010 0.001 PHE D 32 TRP 0.010 0.001 TRP A 112 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 ( 8749) covalent geometry : angle 0.52023 / 0.30 (12371) hydrogen bonds : bond 0.05423 / 3.71 ( 575) hydrogen bonds : angle 3.51381 / 2.60 ( 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 41 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.276 Fit side-chains REVERT: A 89 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8252 (ptm160) REVERT: D 181 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7976 (tttm) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.9886 time to fit residues: 39.3555 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 : 0.304 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085798 restraints weight = 11204.855| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.54 r_work: 0.2993 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8749 Z= 0.157 Angle : 0.528 7.776 12371 Z= 0.303 Chirality : 0.037 0.269 1422 Planarity : 0.004 0.052 1180 Dihedral : 27.777 176.340 2162 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.34 % Allowed : 14.72 % 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 are not related in a simple way. whole: 3.58 (0.31), residues: 758 helix: 2.93 (0.21), residues: 602 sheet: None (None), residues: 0 loop : 0.01 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.014 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/Z covalent geometry : bond 0.00315 / 0.16 ( 8749) covalent geometry : angle 0.52752 / 0.30 (12371) hydrogen bonds : bond 0.05664 / 3.88 ( 575) hydrogen bonds : angle 3.55095 / 2.63 ( 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 40 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.272 Fit side-chains REVERT: A 89 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8250 (ptm160) REVERT: D 181 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7988 (tttm) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.9787 time to fit residues: 38.8080 Evaluate side-chains 40 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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=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: 1.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085955 restraints weight = 11211.896| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.56 r_work: 0.3002 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8749 Z= 0.151 Angle : 0.522 7.583 12371 Z= 0.301 Chirality : 0.037 0.268 1422 Planarity : 0.004 0.053 1180 Dihedral : 27.776 176.392 2162 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.34 % Allowed : 14.72 % 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 are not related in a simple way. whole: 3.65 (0.31), residues: 758 helix: 3.02 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.04 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 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 0.002 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 ( 8749) covalent geometry : angle 0.52239 / 0.30 (12371) hydrogen bonds : bond 0.05546 / 3.80 ( 575) hydrogen bonds : angle 3.52988 / 2.62 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.98 seconds wall clock time: 59 minutes 55.85 seconds (3595.85 seconds total)