Starting phenix.real_space_refine on Thu Jul 2 05:54:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqu_63305/07_2026/9lqu_63305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqu_63305/07_2026/9lqu_63305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lqu_63305/07_2026/9lqu_63305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqu_63305/07_2026/9lqu_63305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lqu_63305/07_2026/9lqu_63305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqu_63305/07_2026/9lqu_63305.map" } resolution = 2.7 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 60 5.16 5 C 4694 2.51 5 N 1018 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6946 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "B" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2184 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "A" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2184 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 324 Unusual residues: {'CLR': 8, 'PCF': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 324 Unusual residues: {'CLR': 8, 'PCF': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 1.65, per 1000 atoms: 0.24 Number of scatterers: 6946 At special positions: 0 Unit cell: (99.51, 53.01, 106.02, 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 60 16.00 P 4 15.00 O 1170 8.00 N 1018 7.00 C 4694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 181 " distance=2.03 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: 0.61 Conformation dependent library (CDL) restraints added in 356.1 milliseconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1508 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 57.8% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'B' and resid 29 through 55 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.628A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 98 through 132 Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.501A pdb=" N TRP B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 193 through 229 removed outlier: 3.753A pdb=" N TRP B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Proline residue: B 213 - end of helix Processing helix chain 'B' and resid 244 through 273 Proline residue: B 263 - end of helix Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 280 through 301 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 304 through 313 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'A' and resid 29 through 55 Processing helix chain 'A' and resid 62 through 80 removed outlier: 3.628A pdb=" N ILE A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 98 through 132 Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.501A pdb=" N TRP A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 Processing helix chain 'A' and resid 193 through 229 removed outlier: 3.754A pdb=" N TRP A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 244 through 273 Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 280 through 301 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 313 through 324 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 13 removed outlier: 7.527A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13 removed outlier: 7.527A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA8, first strand: chain 'A' and resid 168 through 171 438 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 948 1.30 - 1.43: 1911 1.43 - 1.56: 4048 1.56 - 1.69: 153 1.69 - 1.82: 92 Bond restraints: 7152 Sorted by residual: bond pdb=" C21 PCF A 409 " pdb=" O21 PCF A 409 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C21 PCF B 410 " pdb=" O21 PCF B 410 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C31 PCF A 410 " pdb=" O31 PCF A 410 " ideal model delta sigma weight residual 1.329 1.427 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C31 PCF B 409 " pdb=" O31 PCF B 409 " ideal model delta sigma weight residual 1.329 1.427 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C31 PCF A 409 " pdb=" O31 PCF A 409 " ideal model delta sigma weight residual 1.329 1.420 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 7147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 9652 4.71 - 9.43: 130 9.43 - 14.14: 4 14.14 - 18.86: 0 18.86 - 23.57: 4 Bond angle restraints: 9790 Sorted by residual: angle pdb=" O12 PCF A 410 " pdb=" P PCF A 410 " pdb=" O14 PCF A 410 " ideal model delta sigma weight residual 123.69 100.12 23.57 3.00e+00 1.11e-01 6.17e+01 angle pdb=" O12 PCF B 409 " pdb=" P PCF B 409 " pdb=" O14 PCF B 409 " ideal model delta sigma weight residual 123.69 100.17 23.52 3.00e+00 1.11e-01 6.15e+01 angle pdb=" O12 PCF A 409 " pdb=" P PCF A 409 " pdb=" O14 PCF A 409 " ideal model delta sigma weight residual 123.69 101.13 22.56 3.00e+00 1.11e-01 5.66e+01 angle pdb=" O12 PCF B 410 " pdb=" P PCF B 410 " pdb=" O14 PCF B 410 " ideal model delta sigma weight residual 123.69 101.17 22.52 3.00e+00 1.11e-01 5.64e+01 angle pdb=" C32 PCF A 410 " pdb=" C31 PCF A 410 " pdb=" O31 PCF A 410 " ideal model delta sigma weight residual 111.48 122.51 -11.03 3.00e+00 1.11e-01 1.35e+01 ... (remaining 9785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 4788 35.91 - 71.81: 184 71.81 - 107.72: 14 107.72 - 143.63: 4 143.63 - 179.53: 2 Dihedral angle restraints: 4992 sinusoidal: 2638 harmonic: 2354 Sorted by residual: dihedral pdb=" CA ALA D 40 " pdb=" C ALA D 40 " pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta harmonic sigma weight residual 180.00 141.68 38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA ALA C 40 " pdb=" C ALA C 40 " pdb=" N PRO C 41 " pdb=" CA PRO C 41 " ideal model delta harmonic sigma weight residual 180.00 141.68 38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CB CYS D 33 " pdb=" SG CYS D 33 " pdb=" SG CYS D 110 " pdb=" CB CYS D 110 " ideal model delta sinusoidal sigma weight residual -86.00 -36.38 -49.62 1 1.00e+01 1.00e-02 3.38e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 949 0.067 - 0.134: 113 0.134 - 0.201: 36 0.201 - 0.268: 29 0.268 - 0.335: 17 Chirality restraints: 1144 Sorted by residual: chirality pdb=" C17 CLR B 405 " pdb=" C13 CLR B 405 " pdb=" C16 CLR B 405 " pdb=" C20 CLR B 405 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C17 CLR B 404 " pdb=" C13 CLR B 404 " pdb=" C16 CLR B 404 " pdb=" C20 CLR B 404 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C17 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C16 CLR A 405 " pdb=" C20 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1141 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 40 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO D 41 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.059 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO C 41 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 95 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 96 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.016 5.00e-02 4.00e+02 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1133 2.77 - 3.30: 6542 3.30 - 3.83: 12088 3.83 - 4.37: 14313 4.37 - 4.90: 24536 Nonbonded interactions: 58612 Sorted by model distance: nonbonded pdb=" OG SER D 17 " pdb=" OD1 ASN D 83 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 17 " pdb=" OD1 ASN C 83 " model vdw 2.233 3.040 nonbonded pdb=" O PHE A 39 " pdb=" OG1 THR A 43 " model vdw 2.277 3.040 nonbonded pdb=" O PHE B 39 " pdb=" OG1 THR B 43 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 70 " pdb=" NE1 TRP B 154 " model vdw 2.278 3.120 ... (remaining 58607 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 'D' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.050 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: 0.010 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: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.009 0.101 7158 Z= 0.478 Angle : 1.270 23.570 9802 Z= 0.514 Chirality : 0.073 0.335 1144 Planarity : 0.006 0.090 1080 Dihedral : 17.368 179.533 3466 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.27 % Favored : 96.22 % Rotamer: Outliers : 0.59 % Allowed : 18.53 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.78 (0.30), residues: 794 helix: 1.91 (0.26), residues: 442 sheet: -0.27 (0.50), residues: 108 loop : -1.79 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 127 TYR 0.010 0.001 TYR A 264 PHE 0.007 0.001 PHE A 78 TRP 0.007 0.001 TRP B 261 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.48 ( 7152) covalent geometry : angle 1.27032 / 0.51 ( 9790) SS BOND : bond 0.00208 / 0.11 ( 6) SS BOND : angle 1.09939 / 0.79 ( 12) hydrogen bonds : bond 0.14350 / 9.66 ( 426) hydrogen bonds : angle 6.19448 / 4.15 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.293 Fit side-chains REVERT: D 82 MET cc_start: 0.7546 (ptm) cc_final: 0.7332 (ptm) REVERT: B 172 ASP cc_start: 0.8871 (t0) cc_final: 0.8420 (t0) REVERT: A 172 ASP cc_start: 0.8882 (t0) cc_final: 0.8447 (t0) REVERT: A 183 MET cc_start: 0.9115 (tpt) cc_final: 0.8847 (tpt) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.3926 time to fit residues: 39.4682 Evaluate side-chains 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN D 81 GLN B 175 ASN C 81 GLN A 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.173639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132955 restraints weight = 6640.021| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.81 r_work: 0.3313 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7158 Z= 0.162 Angle : 0.692 8.071 9802 Z= 0.328 Chirality : 0.041 0.194 1144 Planarity : 0.006 0.091 1080 Dihedral : 14.398 151.541 2138 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.02 % Favored : 96.47 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.70 (0.30), residues: 794 helix: 1.92 (0.25), residues: 446 sheet: -0.64 (0.47), residues: 110 loop : -1.87 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 168 TYR 0.012 0.002 TYR B 88 PHE 0.010 0.002 PHE B 316 TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7152) covalent geometry : angle 0.69166 / 0.33 ( 9790) SS BOND : bond 0.00267 / 0.15 ( 6) SS BOND : angle 1.06157 / 0.74 ( 12) hydrogen bonds : bond 0.04888 / 3.40 ( 426) hydrogen bonds : angle 4.89004 / 3.31 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 36 MET cc_start: 0.8861 (mmm) cc_final: 0.8660 (mmp) REVERT: B 172 ASP cc_start: 0.9017 (t0) cc_final: 0.8751 (t0) REVERT: A 36 MET cc_start: 0.8861 (mmm) cc_final: 0.8656 (mmp) REVERT: A 172 ASP cc_start: 0.9012 (t0) cc_final: 0.8724 (t0) outliers start: 20 outliers final: 6 residues processed: 105 average time/residue: 0.4563 time to fit residues: 51.0801 Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain A residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 ASN B 175 ASN C 76 ASN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.167278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128261 restraints weight = 6702.064| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.55 r_work: 0.3205 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7158 Z= 0.273 Angle : 0.805 9.930 9802 Z= 0.381 Chirality : 0.046 0.173 1144 Planarity : 0.007 0.095 1080 Dihedral : 14.270 156.142 2138 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.03 % Favored : 95.47 % Rotamer: Outliers : 4.12 % Allowed : 14.41 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.18 (0.29), residues: 794 helix: 1.48 (0.25), residues: 448 sheet: -0.98 (0.44), residues: 112 loop : -2.02 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 55 TYR 0.019 0.002 TYR A 293 PHE 0.017 0.003 PHE B 110 TRP 0.011 0.002 TRP B 85 HIS 0.006 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.27 ( 7152) covalent geometry : angle 0.80303 / 0.38 ( 9790) SS BOND : bond 0.00498 / 0.29 ( 6) SS BOND : angle 1.72486 / 1.12 ( 12) hydrogen bonds : bond 0.05885 / 4.12 ( 426) hydrogen bonds : angle 5.10588 / 3.49 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 156 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (mt) REVERT: B 159 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 159 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 226 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6772 (mt0) outliers start: 28 outliers final: 10 residues processed: 113 average time/residue: 0.3473 time to fit residues: 42.2492 Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN C 76 ASN A 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.173249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133097 restraints weight = 6787.907| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.47 r_work: 0.3278 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7158 Z= 0.136 Angle : 0.609 7.683 9802 Z= 0.296 Chirality : 0.040 0.181 1144 Planarity : 0.006 0.089 1080 Dihedral : 13.317 138.365 2138 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.90 % Favored : 96.60 % Rotamer: Outliers : 3.09 % Allowed : 15.44 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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 (0.30), residues: 794 helix: 1.89 (0.25), residues: 446 sheet: -0.17 (0.45), residues: 104 loop : -2.14 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.013 0.001 TYR D 105 PHE 0.010 0.001 PHE A 100 TRP 0.010 0.001 TRP B 51 HIS 0.005 0.002 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 7152) covalent geometry : angle 0.60846 / 0.30 ( 9790) SS BOND : bond 0.00214 / 0.13 ( 6) SS BOND : angle 1.06655 / 0.76 ( 12) hydrogen bonds : bond 0.04527 / 3.13 ( 426) hydrogen bonds : angle 4.60015 / 3.14 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.244 Fit side-chains REVERT: B 156 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 172 ASP cc_start: 0.8998 (t0) cc_final: 0.8789 (t0) REVERT: B 226 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: B 268 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7964 (ttpt) REVERT: A 172 ASP cc_start: 0.9000 (t0) cc_final: 0.8797 (t0) REVERT: A 226 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6895 (mt0) outliers start: 21 outliers final: 6 residues processed: 100 average time/residue: 0.3736 time to fit residues: 40.1735 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132493 restraints weight = 6802.358| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.51 r_work: 0.3234 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7158 Z= 0.176 Angle : 0.647 9.084 9802 Z= 0.313 Chirality : 0.041 0.185 1144 Planarity : 0.006 0.090 1080 Dihedral : 12.952 129.917 2138 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.02 % Favored : 96.47 % Rotamer: Outliers : 2.94 % Allowed : 15.74 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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 (0.30), residues: 794 helix: 1.95 (0.25), residues: 446 sheet: -0.31 (0.44), residues: 104 loop : -2.23 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.013 0.002 TYR D 105 PHE 0.013 0.002 PHE A 110 TRP 0.007 0.001 TRP B 85 HIS 0.006 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 7152) covalent geometry : angle 0.64588 / 0.31 ( 9790) SS BOND : bond 0.00343 / 0.20 ( 6) SS BOND : angle 1.36487 / 0.92 ( 12) hydrogen bonds : bond 0.04959 / 3.46 ( 426) hydrogen bonds : angle 4.65551 / 3.17 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.242 Fit side-chains REVERT: B 156 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 159 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8543 (mp) REVERT: B 226 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6882 (mt0) REVERT: A 159 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 226 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6825 (mt0) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.3900 time to fit residues: 41.1834 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.172701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134469 restraints weight = 6796.875| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.54 r_work: 0.3210 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7158 Z= 0.144 Angle : 0.605 8.229 9802 Z= 0.294 Chirality : 0.040 0.180 1144 Planarity : 0.006 0.088 1080 Dihedral : 12.333 121.388 2138 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.02 % Favored : 96.47 % Rotamer: Outliers : 3.24 % Allowed : 15.59 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.76 (0.30), residues: 794 helix: 2.09 (0.25), residues: 446 sheet: -0.31 (0.44), residues: 104 loop : -2.24 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.012 0.001 TYR D 105 PHE 0.010 0.002 PHE A 110 TRP 0.008 0.001 TRP B 51 HIS 0.006 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7152) covalent geometry : angle 0.60409 / 0.29 ( 9790) SS BOND : bond 0.00239 / 0.14 ( 6) SS BOND : angle 1.10067 / 0.77 ( 12) hydrogen bonds : bond 0.04586 / 3.17 ( 426) hydrogen bonds : angle 4.52256 / 3.08 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.249 Fit side-chains REVERT: B 156 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8190 (mt) REVERT: B 159 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8524 (mp) REVERT: B 172 ASP cc_start: 0.8987 (t0) cc_final: 0.8770 (t0) REVERT: B 183 MET cc_start: 0.9100 (tpt) cc_final: 0.8637 (tpt) REVERT: B 226 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: A 159 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 172 ASP cc_start: 0.8971 (t0) cc_final: 0.8754 (t0) REVERT: A 226 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6856 (mt0) outliers start: 22 outliers final: 10 residues processed: 99 average time/residue: 0.3571 time to fit residues: 38.2990 Evaluate side-chains 101 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.171808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132148 restraints weight = 6801.366| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.59 r_work: 0.3275 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7158 Z= 0.138 Angle : 0.596 8.377 9802 Z= 0.289 Chirality : 0.039 0.182 1144 Planarity : 0.006 0.087 1080 Dihedral : 12.017 119.769 2138 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.64 % Favored : 96.85 % Rotamer: Outliers : 2.94 % Allowed : 16.03 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.85 (0.30), residues: 794 helix: 2.18 (0.25), residues: 446 sheet: -0.32 (0.44), residues: 104 loop : -2.23 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.011 0.001 TYR B 88 PHE 0.011 0.001 PHE A 110 TRP 0.007 0.001 TRP B 51 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7152) covalent geometry : angle 0.59452 / 0.29 ( 9790) SS BOND : bond 0.00217 / 0.13 ( 6) SS BOND : angle 1.18148 / 0.83 ( 12) hydrogen bonds : bond 0.04471 / 3.10 ( 426) hydrogen bonds : angle 4.46668 / 3.04 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.164 Fit side-chains REVERT: B 36 MET cc_start: 0.8892 (mmm) cc_final: 0.8655 (mmp) REVERT: B 156 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 159 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 172 ASP cc_start: 0.8982 (t0) cc_final: 0.8770 (t0) REVERT: B 226 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6896 (mt0) REVERT: A 36 MET cc_start: 0.8885 (mmm) cc_final: 0.8681 (mmp) REVERT: A 159 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8568 (mp) REVERT: A 172 ASP cc_start: 0.8987 (t0) cc_final: 0.8775 (t0) REVERT: A 226 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (mt0) outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 0.3219 time to fit residues: 31.9616 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.170452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128673 restraints weight = 6689.826| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.75 r_work: 0.3239 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7158 Z= 0.156 Angle : 0.613 8.691 9802 Z= 0.297 Chirality : 0.040 0.183 1144 Planarity : 0.006 0.087 1080 Dihedral : 11.849 117.961 2138 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.90 % Favored : 96.60 % Rotamer: Outliers : 2.79 % Allowed : 16.62 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.79 (0.30), residues: 794 helix: 2.12 (0.25), residues: 446 sheet: -0.34 (0.44), residues: 104 loop : -2.24 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 245 TYR 0.012 0.001 TYR A 293 PHE 0.013 0.002 PHE A 110 TRP 0.007 0.001 TRP B 85 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7152) covalent geometry : angle 0.61220 / 0.30 ( 9790) SS BOND : bond 0.00254 / 0.15 ( 6) SS BOND : angle 1.16293 / 0.80 ( 12) hydrogen bonds : bond 0.04657 / 3.23 ( 426) hydrogen bonds : angle 4.51798 / 3.08 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.240 Fit side-chains REVERT: B 156 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (mt) REVERT: B 159 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8594 (mp) REVERT: B 172 ASP cc_start: 0.9001 (t0) cc_final: 0.8796 (t0) REVERT: B 226 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: A 159 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8601 (mp) REVERT: A 172 ASP cc_start: 0.8992 (t0) cc_final: 0.8786 (t0) REVERT: A 226 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6892 (mt0) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 0.3265 time to fit residues: 32.8261 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.172847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134782 restraints weight = 6713.637| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.49 r_work: 0.3263 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7158 Z= 0.129 Angle : 0.586 8.109 9802 Z= 0.285 Chirality : 0.039 0.182 1144 Planarity : 0.006 0.086 1080 Dihedral : 11.546 115.098 2134 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.52 % Favored : 96.98 % Rotamer: Outliers : 2.50 % Allowed : 16.62 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.91 (0.30), residues: 794 helix: 2.23 (0.25), residues: 446 sheet: -0.28 (0.44), residues: 104 loop : -2.21 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.010 0.001 TYR B 88 PHE 0.010 0.001 PHE B 110 TRP 0.007 0.001 TRP B 51 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 7152) covalent geometry : angle 0.58504 / 0.28 ( 9790) SS BOND : bond 0.00175 / 0.10 ( 6) SS BOND : angle 1.09685 / 0.78 ( 12) hydrogen bonds : bond 0.04337 / 2.99 ( 426) hydrogen bonds : angle 4.39820 / 2.99 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.247 Fit side-chains REVERT: B 156 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 159 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 172 ASP cc_start: 0.8952 (t0) cc_final: 0.8749 (t0) REVERT: B 183 MET cc_start: 0.9066 (tpt) cc_final: 0.8605 (tpt) REVERT: B 226 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: A 159 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 172 ASP cc_start: 0.8951 (t0) cc_final: 0.8742 (t0) REVERT: A 183 MET cc_start: 0.9042 (tpt) cc_final: 0.8555 (tpt) REVERT: A 226 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6874 (mt0) outliers start: 17 outliers final: 8 residues processed: 90 average time/residue: 0.3518 time to fit residues: 34.0943 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.170384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129146 restraints weight = 6749.632| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.68 r_work: 0.3211 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7158 Z= 0.167 Angle : 0.635 9.045 9802 Z= 0.307 Chirality : 0.041 0.187 1144 Planarity : 0.006 0.086 1080 Dihedral : 11.621 115.973 2134 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.27 % Favored : 96.22 % Rotamer: Outliers : 2.21 % Allowed : 17.35 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.79 (0.30), residues: 794 helix: 2.14 (0.25), residues: 446 sheet: -0.35 (0.44), residues: 104 loop : -2.27 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 55 TYR 0.014 0.001 TYR B 293 PHE 0.015 0.002 PHE A 110 TRP 0.008 0.001 TRP B 85 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7152) covalent geometry : angle 0.63375 / 0.31 ( 9790) SS BOND : bond 0.00270 / 0.16 ( 6) SS BOND : angle 1.30237 / 0.92 ( 12) hydrogen bonds : bond 0.04789 / 3.32 ( 426) hydrogen bonds : angle 4.55098 / 3.10 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.156 Fit side-chains REVERT: B 156 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8261 (mt) REVERT: B 159 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8553 (mp) REVERT: B 172 ASP cc_start: 0.8997 (t0) cc_final: 0.8794 (t0) REVERT: B 183 MET cc_start: 0.9097 (tpt) cc_final: 0.8566 (tpt) REVERT: B 226 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: A 159 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 226 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6857 (mt0) outliers start: 15 outliers final: 8 residues processed: 94 average time/residue: 0.3712 time to fit residues: 37.6973 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 226 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN B 175 ASN C 39 GLN A 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.170978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131259 restraints weight = 6695.790| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.56 r_work: 0.3238 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7158 Z= 0.153 Angle : 0.623 8.610 9802 Z= 0.303 Chirality : 0.040 0.184 1144 Planarity : 0.006 0.085 1080 Dihedral : 11.528 113.950 2134 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.90 % Favored : 96.60 % Rotamer: Outliers : 2.21 % Allowed : 17.06 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % 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: 0.82 (0.30), residues: 794 helix: 2.15 (0.25), residues: 446 sheet: -0.31 (0.44), residues: 104 loop : -2.24 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 245 TYR 0.012 0.001 TYR B 88 PHE 0.012 0.002 PHE A 110 TRP 0.008 0.001 TRP B 85 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7152) covalent geometry : angle 0.62228 / 0.30 ( 9790) SS BOND : bond 0.00240 / 0.14 ( 6) SS BOND : angle 1.20762 / 0.85 ( 12) hydrogen bonds : bond 0.04617 / 3.19 ( 426) hydrogen bonds : angle 4.49637 / 3.06 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.88 seconds wall clock time: 38 minutes 36.23 seconds (2316.23 seconds total)