Starting phenix.real_space_refine on Thu Sep 10 22:21:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nt5_0502/09_2026/6nt5_0502_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nt5_0502/09_2026/6nt5_0502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nt5_0502/09_2026/6nt5_0502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nt5_0502/09_2026/6nt5_0502.map" model { file = "/net/cci-nas-00/data/ceres_data/6nt5_0502/09_2026/6nt5_0502_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nt5_0502/09_2026/6nt5_0502_neut.cif" } resolution = 4.1 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= 0.003 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 2952 2.51 5 N 798 2.21 5 O 812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4586 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2293 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Restraints were copied for chains: B Time building chain proxies: 1.47, per 1000 atoms: 0.32 Number of scatterers: 4586 At special positions: 0 Unit cell: (78.12, 73.08, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 812 8.00 N 798 7.00 C 2952 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: 0.31 Conformation dependent library (CDL) restraints added in 121.0 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 60.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.846A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 70 removed outlier: 3.763A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.612A pdb=" N ARG A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.765A pdb=" N LEU A 123 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.684A pdb=" N ALA A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.134A pdb=" N ASN A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 4.179A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.528A pdb=" N ALA A 277 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 278 " --> pdb=" O SER A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 278' Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.746A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.699A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 33 removed outlier: 3.846A pdb=" N LEU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 70 removed outlier: 3.762A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.612A pdb=" N ARG B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 134 removed outlier: 3.766A pdb=" N LEU B 123 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 156 through 167 removed outlier: 3.683A pdb=" N ALA B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.134A pdb=" N ASN B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.179A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.529A pdb=" N ALA B 277 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 278 " --> pdb=" O SER B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 278' Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.748A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.699A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223 removed outlier: 5.944A pdb=" N PHE A 221 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU A 246 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 223 removed outlier: 5.945A pdb=" N PHE B 221 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU B 246 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR B 314 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 202 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1437 1.34 - 1.45: 710 1.45 - 1.57: 2501 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4676 Sorted by residual: bond pdb=" CA GLY B 90 " pdb=" C GLY B 90 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.04e-02 9.25e+03 3.67e+00 bond pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.04e-02 9.25e+03 3.50e+00 bond pdb=" N GLY B 90 " pdb=" CA GLY B 90 " ideal model delta sigma weight residual 1.464 1.447 0.018 1.12e-02 7.97e+03 2.44e+00 bond pdb=" N GLY A 90 " pdb=" CA GLY A 90 " ideal model delta sigma weight residual 1.464 1.447 0.017 1.12e-02 7.97e+03 2.36e+00 bond pdb=" C PRO A 11 " pdb=" N CYS A 12 " ideal model delta sigma weight residual 1.329 1.300 0.029 1.86e-02 2.89e+03 2.35e+00 ... (remaining 4671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 6141 2.26 - 4.52: 171 4.52 - 6.79: 18 6.79 - 9.05: 10 9.05 - 11.31: 2 Bond angle restraints: 6342 Sorted by residual: angle pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" C LEU B 172 " ideal model delta sigma weight residual 109.81 121.12 -11.31 2.21e+00 2.05e-01 2.62e+01 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" C LEU A 172 " ideal model delta sigma weight residual 109.81 121.11 -11.30 2.21e+00 2.05e-01 2.62e+01 angle pdb=" C GLY B 151 " pdb=" N ASN B 152 " pdb=" CA ASN B 152 " ideal model delta sigma weight residual 122.08 128.79 -6.71 1.47e+00 4.63e-01 2.09e+01 angle pdb=" C GLY A 151 " pdb=" N ASN A 152 " pdb=" CA ASN A 152 " ideal model delta sigma weight residual 122.08 128.75 -6.67 1.47e+00 4.63e-01 2.06e+01 angle pdb=" C PRO A 11 " pdb=" N CYS A 12 " pdb=" CA CYS A 12 " ideal model delta sigma weight residual 121.48 129.66 -8.18 2.04e+00 2.40e-01 1.61e+01 ... (remaining 6337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 2634 14.52 - 29.04: 108 29.04 - 43.56: 34 43.56 - 58.08: 3 58.08 - 72.60: 7 Dihedral angle restraints: 2786 sinusoidal: 1086 harmonic: 1700 Sorted by residual: dihedral pdb=" CA ASP B 223 " pdb=" C ASP B 223 " pdb=" N LYS B 224 " pdb=" CA LYS B 224 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR A 245 " pdb=" C TYR A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 559 0.055 - 0.109: 141 0.109 - 0.164: 24 0.164 - 0.218: 2 0.218 - 0.273: 4 Chirality restraints: 730 Sorted by residual: chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU B 172 " pdb=" N LEU B 172 " pdb=" C LEU B 172 " pdb=" CB LEU B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN A 152 " pdb=" N ASN A 152 " pdb=" C ASN A 152 " pdb=" CB ASN A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 727 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 172 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 173 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 172 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 173 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 7 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 8 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " 0.027 5.00e-02 4.00e+02 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1337 2.82 - 3.34: 4039 3.34 - 3.86: 7068 3.86 - 4.38: 7543 4.38 - 4.90: 13049 Nonbonded interactions: 33036 Sorted by model distance: nonbonded pdb=" O TYR A 81 " pdb=" OG1 THR A 84 " model vdw 2.300 3.040 nonbonded pdb=" O TYR B 81 " pdb=" OG1 THR B 84 " model vdw 2.301 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.388 3.040 nonbonded pdb=" O LEU B 124 " pdb=" OG SER B 127 " model vdw 2.390 3.040 nonbonded pdb=" O HIS A 50 " pdb=" OG SER A 53 " model vdw 2.461 3.040 ... (remaining 33031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.006 0.055 4676 Z= 0.296 Angle : 0.931 11.310 6342 Z= 0.495 Chirality : 0.053 0.273 730 Planarity : 0.008 0.054 798 Dihedral : 10.321 72.601 1686 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.41 % Allowed : 1.23 % Favored : 98.35 % 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: -2.40 (0.29), residues: 552 helix: -1.14 (0.24), residues: 304 sheet: -1.41 (0.79), residues: 28 loop : -2.13 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 178 TYR 0.032 0.003 TYR B 199 PHE 0.019 0.003 PHE A 153 TRP 0.007 0.002 TRP B 82 HIS 0.007 0.002 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.30 ( 4676) covalent geometry : angle 0.93095 / 0.49 ( 6342) hydrogen bonds : bond 0.10373 / 6.52 ( 236) hydrogen bonds : angle 5.57110 / 3.81 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.8972 (t0) cc_final: 0.8580 (t0) REVERT: A 93 LEU cc_start: 0.8599 (mt) cc_final: 0.8245 (pp) REVERT: A 119 TRP cc_start: 0.7263 (p90) cc_final: 0.7051 (p90) REVERT: A 183 ASN cc_start: 0.7717 (m-40) cc_final: 0.6848 (p0) REVERT: A 223 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: B 61 ASN cc_start: 0.8980 (t0) cc_final: 0.8584 (t0) REVERT: B 93 LEU cc_start: 0.8635 (mt) cc_final: 0.8278 (pp) REVERT: B 104 TYR cc_start: 0.7430 (t80) cc_final: 0.7212 (t80) REVERT: B 154 ASN cc_start: 0.8612 (t0) cc_final: 0.8310 (p0) REVERT: B 183 ASN cc_start: 0.7658 (m-40) cc_final: 0.6803 (p0) REVERT: B 223 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7877 (m-30) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.0535 time to fit residues: 9.1343 Evaluate side-chains 51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN B 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066807 restraints weight = 19485.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068595 restraints weight = 10615.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069753 restraints weight = 7027.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070516 restraints weight = 5302.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.071075 restraints weight = 4366.960| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4676 Z= 0.129 Angle : 0.572 6.793 6342 Z= 0.284 Chirality : 0.041 0.139 730 Planarity : 0.005 0.035 798 Dihedral : 4.657 17.123 638 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.06 (0.35), residues: 552 helix: 1.04 (0.29), residues: 318 sheet: -0.40 (0.87), residues: 28 loop : -1.47 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.016 0.001 TYR B 199 PHE 0.008 0.001 PHE B 117 TRP 0.004 0.001 TRP A 161 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4676) covalent geometry : angle 0.57229 / 0.28 ( 6342) hydrogen bonds : bond 0.03386 / 2.41 ( 236) hydrogen bonds : angle 3.89185 / 2.70 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASN cc_start: 0.7734 (m-40) cc_final: 0.6927 (p0) REVERT: B 155 VAL cc_start: 0.9137 (t) cc_final: 0.8735 (p) REVERT: B 183 ASN cc_start: 0.7566 (m-40) cc_final: 0.6753 (p0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0444 time to fit residues: 5.2880 Evaluate side-chains 40 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.081203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068297 restraints weight = 18937.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070056 restraints weight = 10609.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.071228 restraints weight = 7031.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072053 restraints weight = 5263.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.072492 restraints weight = 4262.816| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4676 Z= 0.094 Angle : 0.516 6.029 6342 Z= 0.254 Chirality : 0.039 0.180 730 Planarity : 0.004 0.027 798 Dihedral : 4.164 15.469 638 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: 1.00 (0.36), residues: 552 helix: 1.80 (0.30), residues: 318 sheet: 0.10 (0.89), residues: 28 loop : -1.11 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.012 0.001 TYR B 261 PHE 0.007 0.001 PHE A 279 TRP 0.005 0.001 TRP B 119 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 4676) covalent geometry : angle 0.51562 / 0.25 ( 6342) hydrogen bonds : bond 0.02637 / 1.84 ( 236) hydrogen bonds : angle 3.49211 / 2.43 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 VAL cc_start: 0.9066 (t) cc_final: 0.8657 (p) REVERT: B 208 VAL cc_start: 0.9193 (t) cc_final: 0.8938 (t) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0552 time to fit residues: 5.0227 Evaluate side-chains 38 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.077811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064803 restraints weight = 19066.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066510 restraints weight = 10549.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067671 restraints weight = 7040.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068383 restraints weight = 5294.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068929 restraints weight = 4363.526| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4676 Z= 0.229 Angle : 0.645 6.043 6342 Z= 0.316 Chirality : 0.042 0.135 730 Planarity : 0.004 0.029 798 Dihedral : 4.409 15.579 638 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 1.05 (0.37), residues: 552 helix: 1.76 (0.30), residues: 320 sheet: -0.14 (0.93), residues: 28 loop : -0.89 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 197 TYR 0.017 0.002 TYR A 199 PHE 0.012 0.002 PHE B 269 TRP 0.006 0.001 TRP A 119 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 ( 4676) covalent geometry : angle 0.64479 / 0.32 ( 6342) hydrogen bonds : bond 0.03734 / 2.61 ( 236) hydrogen bonds : angle 3.93871 / 2.78 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 VAL cc_start: 0.9165 (t) cc_final: 0.8780 (p) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0698 time to fit residues: 4.5920 Evaluate side-chains 29 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS B 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063218 restraints weight = 19538.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064873 restraints weight = 10704.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065957 restraints weight = 7132.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066718 restraints weight = 5431.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067226 restraints weight = 4471.061| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 4676 Z= 0.254 Angle : 0.688 7.368 6342 Z= 0.336 Chirality : 0.043 0.150 730 Planarity : 0.004 0.030 798 Dihedral : 4.682 15.111 638 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: 0.66 (0.37), residues: 552 helix: 1.43 (0.29), residues: 322 sheet: -0.76 (0.78), residues: 46 loop : -0.98 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.017 0.002 TYR B 199 PHE 0.016 0.002 PHE A 269 TRP 0.010 0.002 TRP A 119 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 ( 4676) covalent geometry : angle 0.68804 / 0.34 ( 6342) hydrogen bonds : bond 0.04184 / 2.96 ( 236) hydrogen bonds : angle 4.22732 / 2.97 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.185 Fit side-chains REVERT: A 104 TYR cc_start: 0.7382 (t80) cc_final: 0.7129 (t80) REVERT: A 149 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 155 VAL cc_start: 0.9209 (t) cc_final: 0.8854 (p) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0601 time to fit residues: 4.0012 Evaluate side-chains 27 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 55 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.1446 > 50:) chunk 12 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066250 restraints weight = 19169.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068002 restraints weight = 10422.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069240 restraints weight = 6797.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.070096 restraints weight = 5063.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070639 restraints weight = 4069.526| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4676 Z= 0.100 Angle : 0.508 5.911 6342 Z= 0.250 Chirality : 0.039 0.178 730 Planarity : 0.003 0.030 798 Dihedral : 4.135 15.417 638 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.25 (0.38), residues: 552 helix: 2.00 (0.30), residues: 322 sheet: -0.75 (0.77), residues: 46 loop : -0.87 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.011 0.001 TYR A 199 PHE 0.009 0.001 PHE A 117 TRP 0.011 0.001 TRP A 119 HIS 0.005 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 4676) covalent geometry : angle 0.50849 / 0.25 ( 6342) hydrogen bonds : bond 0.02966 / 2.09 ( 236) hydrogen bonds : angle 3.55613 / 2.48 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 119 TRP cc_start: 0.7568 (p90) cc_final: 0.6918 (p90) REVERT: B 154 ASN cc_start: 0.8656 (t0) cc_final: 0.8449 (p0) REVERT: B 155 VAL cc_start: 0.9103 (t) cc_final: 0.8717 (p) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0506 time to fit residues: 3.8502 Evaluate side-chains 29 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.075642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.062541 restraints weight = 19891.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064171 restraints weight = 11031.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065244 restraints weight = 7444.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066044 restraints weight = 5661.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066548 restraints weight = 4647.539| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4676 Z= 0.278 Angle : 0.720 7.041 6342 Z= 0.351 Chirality : 0.045 0.169 730 Planarity : 0.004 0.031 798 Dihedral : 4.588 14.732 638 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 0.65 (0.37), residues: 552 helix: 1.53 (0.30), residues: 320 sheet: -0.97 (0.77), residues: 46 loop : -1.13 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 197 TYR 0.017 0.002 TYR A 199 PHE 0.017 0.002 PHE B 269 TRP 0.012 0.002 TRP B 119 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 ( 4676) covalent geometry : angle 0.72016 / 0.35 ( 6342) hydrogen bonds : bond 0.04251 / 3.01 ( 236) hydrogen bonds : angle 4.19918 / 2.97 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 155 VAL cc_start: 0.9301 (t) cc_final: 0.8951 (p) REVERT: B 155 VAL cc_start: 0.9286 (t) cc_final: 0.8932 (p) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0456 time to fit residues: 3.0619 Evaluate side-chains 27 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066186 restraints weight = 19386.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067917 restraints weight = 10562.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069171 restraints weight = 6886.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.069950 restraints weight = 5090.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070513 restraints weight = 4131.973| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4676 Z= 0.096 Angle : 0.531 6.699 6342 Z= 0.256 Chirality : 0.039 0.132 730 Planarity : 0.003 0.030 798 Dihedral : 4.063 15.347 638 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.10 (0.38), residues: 552 helix: 1.89 (0.30), residues: 320 sheet: -0.85 (0.75), residues: 46 loop : -0.91 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.010 0.001 TYR A 199 PHE 0.004 0.001 PHE A 279 TRP 0.011 0.001 TRP A 119 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 4676) covalent geometry : angle 0.53070 / 0.26 ( 6342) hydrogen bonds : bond 0.02984 / 2.12 ( 236) hydrogen bonds : angle 3.58294 / 2.53 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 VAL cc_start: 0.9210 (t) cc_final: 0.8871 (p) REVERT: A 223 ASP cc_start: 0.8106 (t0) cc_final: 0.7517 (t70) REVERT: B 119 TRP cc_start: 0.7619 (p90) cc_final: 0.6917 (p90) REVERT: B 155 VAL cc_start: 0.9149 (t) cc_final: 0.8801 (p) REVERT: B 223 ASP cc_start: 0.8097 (t0) cc_final: 0.7524 (t70) REVERT: B 296 GLU cc_start: 0.8019 (pt0) cc_final: 0.7707 (tt0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0481 time to fit residues: 3.5836 Evaluate side-chains 32 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067436 restraints weight = 19513.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.069247 restraints weight = 10500.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.070384 restraints weight = 6898.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071025 restraints weight = 5185.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071694 restraints weight = 4319.413| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4676 Z= 0.091 Angle : 0.519 6.928 6342 Z= 0.250 Chirality : 0.038 0.130 730 Planarity : 0.004 0.060 798 Dihedral : 3.858 15.378 638 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.40 (0.38), residues: 552 helix: 2.10 (0.30), residues: 320 sheet: -0.69 (0.74), residues: 46 loop : -0.72 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 293 TYR 0.011 0.001 TYR A 261 PHE 0.006 0.001 PHE A 153 TRP 0.006 0.000 TRP A 161 HIS 0.003 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 4676) covalent geometry : angle 0.51860 / 0.25 ( 6342) hydrogen bonds : bond 0.02711 / 1.92 ( 236) hydrogen bonds : angle 3.49651 / 2.43 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9148 (mm) cc_final: 0.8895 (tt) REVERT: A 154 ASN cc_start: 0.8544 (t0) cc_final: 0.8096 (t0) REVERT: A 155 VAL cc_start: 0.9131 (t) cc_final: 0.8749 (p) REVERT: A 223 ASP cc_start: 0.8099 (t0) cc_final: 0.7452 (t70) REVERT: B 119 TRP cc_start: 0.7634 (p90) cc_final: 0.6846 (p90) REVERT: B 155 VAL cc_start: 0.8881 (t) cc_final: 0.8442 (p) REVERT: B 223 ASP cc_start: 0.8129 (t0) cc_final: 0.7498 (t70) REVERT: B 296 GLU cc_start: 0.8137 (pt0) cc_final: 0.7859 (tt0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0471 time to fit residues: 3.7808 Evaluate side-chains 34 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 20.0000 chunk 6 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 0.0010 chunk 37 optimal weight: 0.9980 overall best weight: 0.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068510 restraints weight = 19416.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070164 restraints weight = 10840.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071289 restraints weight = 7273.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072037 restraints weight = 5555.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072450 restraints weight = 4568.046| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4676 Z= 0.087 Angle : 0.513 7.025 6342 Z= 0.245 Chirality : 0.038 0.124 730 Planarity : 0.003 0.030 798 Dihedral : 3.756 15.580 638 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.62 (0.38), residues: 552 helix: 2.20 (0.30), residues: 324 sheet: -0.51 (0.73), residues: 46 loop : -0.55 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.010 0.001 TYR A 261 PHE 0.004 0.001 PHE B 153 TRP 0.011 0.001 TRP B 119 HIS 0.005 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 ( 4676) covalent geometry : angle 0.51255 / 0.25 ( 6342) hydrogen bonds : bond 0.02555 / 1.82 ( 236) hydrogen bonds : angle 3.44044 / 2.39 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9167 (mm) cc_final: 0.8907 (tt) REVERT: A 119 TRP cc_start: 0.7482 (p90) cc_final: 0.6796 (p90) REVERT: A 223 ASP cc_start: 0.8034 (t0) cc_final: 0.7433 (t70) REVERT: B 155 VAL cc_start: 0.8869 (t) cc_final: 0.8443 (p) REVERT: B 223 ASP cc_start: 0.8043 (t0) cc_final: 0.7466 (t70) REVERT: B 296 GLU cc_start: 0.7962 (pt0) cc_final: 0.7743 (tt0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0438 time to fit residues: 3.6906 Evaluate side-chains 33 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067888 restraints weight = 19710.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069625 restraints weight = 10869.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070848 restraints weight = 7216.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071363 restraints weight = 5438.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072066 restraints weight = 4649.799| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4676 Z= 0.089 Angle : 0.515 6.536 6342 Z= 0.252 Chirality : 0.038 0.138 730 Planarity : 0.003 0.030 798 Dihedral : 3.704 15.287 638 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.79 (0.38), residues: 552 helix: 2.13 (0.30), residues: 324 sheet: 0.39 (0.89), residues: 28 loop : -0.25 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.009 0.001 TYR A 199 PHE 0.003 0.001 PHE A 279 TRP 0.005 0.001 TRP B 119 HIS 0.007 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 4676) covalent geometry : angle 0.51539 / 0.25 ( 6342) hydrogen bonds : bond 0.02677 / 1.92 ( 236) hydrogen bonds : angle 3.43188 / 2.40 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 801.68 seconds wall clock time: 14 minutes 28.38 seconds (868.38 seconds total)