Starting phenix.real_space_refine on Tue Jan 13 09:55:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpe_36477/01_2026/8jpe_36477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpe_36477/01_2026/8jpe_36477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpe_36477/01_2026/8jpe_36477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpe_36477/01_2026/8jpe_36477.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpe_36477/01_2026/8jpe_36477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpe_36477/01_2026/8jpe_36477.cif" } resolution = 2.91 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= 0.027 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 7 5.16 5 C 1390 2.51 5 N 376 2.21 5 O 408 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2189 Number of models: 1 Model: "" Number of chains: 3 Chain: "Q" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2155 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 11, 'TRANS': 305} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 14, 'ARG:plan': 11, 'PHE:plan': 5, 'GLN:plan1': 9, 'TYR:plan': 6, 'HIS:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 328 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.73, per 1000 atoms: 0.33 Number of scatterers: 2189 At special positions: 0 Unit cell: (59.328, 79.928, 56.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 7 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 408 8.00 N 376 7.00 C 1390 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: 0.80 Conformation dependent library (CDL) restraints added in 55.7 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 62.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'Q' and resid 51 through 64 Processing helix chain 'Q' and resid 68 through 98 removed outlier: 4.053A pdb=" N LYS Q 77 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU Q 78 " --> pdb=" O GLY Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.563A pdb=" N LYS Q 107 " --> pdb=" O TYR Q 103 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA Q 108 " --> pdb=" O GLU Q 104 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS Q 109 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 138 removed outlier: 3.790A pdb=" N ASP Q 130 " --> pdb=" O ASN Q 126 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA Q 131 " --> pdb=" O PRO Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 147 Processing helix chain 'Q' and resid 148 through 151 Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 164 through 169 Processing helix chain 'Q' and resid 175 through 181 Processing helix chain 'Q' and resid 209 through 214 removed outlier: 4.251A pdb=" N ARG Q 214 " --> pdb=" O ARG Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 removed outlier: 3.875A pdb=" N HIS Q 218 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE Q 220 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 236 removed outlier: 3.602A pdb=" N ASP Q 236 " --> pdb=" O SER Q 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 233 through 236' Processing helix chain 'Q' and resid 246 through 261 Processing helix chain 'Q' and resid 262 through 265 Processing helix chain 'Q' and resid 275 through 286 removed outlier: 4.074A pdb=" N GLU Q 281 " --> pdb=" O ASP Q 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET Q 284 " --> pdb=" O GLU Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 292 removed outlier: 4.122A pdb=" N TYR Q 291 " --> pdb=" O HIS Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 316 removed outlier: 3.791A pdb=" N LEU Q 316 " --> pdb=" O MET Q 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 333 through 352 removed outlier: 3.651A pdb=" N ALA Q 343 " --> pdb=" O PHE Q 339 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP Q 346 " --> pdb=" O ALA Q 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 190 through 192 removed outlier: 5.954A pdb=" N LEU Q 40 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL Q 204 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU Q 42 " --> pdb=" O VAL Q 204 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS Q 41 " --> pdb=" O SER Q 225 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N MET Q 227 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU Q 43 " --> pdb=" O MET Q 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU Q 229 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU Q 45 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA Q 231 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER Q 268 " --> pdb=" O THR Q 224 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 372 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: 0.31 Time building geometry restraints manager: 0.22 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: 719 1.34 - 1.46: 343 1.46 - 1.58: 1147 1.58 - 1.69: 3 1.69 - 1.81: 16 Bond restraints: 2228 Sorted by residual: bond pdb=" F1 ALF Q 403 " pdb="AL ALF Q 403 " ideal model delta sigma weight residual 1.684 1.800 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" F2 ALF Q 403 " pdb="AL ALF Q 403 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" F3 ALF Q 403 " pdb="AL ALF Q 403 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" F4 ALF Q 403 " pdb="AL ALF Q 403 " ideal model delta sigma weight residual 1.686 1.800 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" N ARG Q 38 " pdb=" CA ARG Q 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 2223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 3057 14.25 - 28.51: 4 28.51 - 42.76: 0 42.76 - 57.01: 0 57.01 - 71.27: 2 Bond angle restraints: 3063 Sorted by residual: angle pdb=" F1 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F2 ALF Q 403 " ideal model delta sigma weight residual 108.68 179.95 -71.27 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F4 ALF Q 403 " ideal model delta sigma weight residual 109.63 179.99 -70.36 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F4 ALF Q 403 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F3 ALF Q 403 " ideal model delta sigma weight residual 109.69 90.02 19.67 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F3 ALF Q 403 " ideal model delta sigma weight residual 109.59 89.99 19.60 3.00e+00 1.11e-01 4.27e+01 ... (remaining 3058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 1248 22.70 - 45.40: 59 45.40 - 68.10: 4 68.10 - 90.79: 1 90.79 - 113.49: 1 Dihedral angle restraints: 1313 sinusoidal: 374 harmonic: 939 Sorted by residual: dihedral pdb=" O2B GDP Q 401 " pdb=" O3A GDP Q 401 " pdb=" PB GDP Q 401 " pdb=" PA GDP Q 401 " ideal model delta sinusoidal sigma weight residual 180.00 66.51 113.49 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" CA ASN Q 82 " pdb=" CB ASN Q 82 " pdb=" CG ASN Q 82 " pdb=" OD1 ASN Q 82 " ideal model delta sinusoidal sigma weight residual 120.00 -169.90 -70.10 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA GLN Q 81 " pdb=" CB GLN Q 81 " pdb=" CG GLN Q 81 " pdb=" CD GLN Q 81 " ideal model delta sinusoidal sigma weight residual 60.00 114.89 -54.89 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 1310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 229 0.026 - 0.052: 90 0.052 - 0.077: 31 0.077 - 0.103: 13 0.103 - 0.129: 15 Chirality restraints: 378 Sorted by residual: chirality pdb=" CA ILE Q 324 " pdb=" N ILE Q 324 " pdb=" C ILE Q 324 " pdb=" CB ILE Q 324 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE Q 270 " pdb=" N ILE Q 270 " pdb=" C ILE Q 270 " pdb=" CB ILE Q 270 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE Q 190 " pdb=" N ILE Q 190 " pdb=" C ILE Q 190 " pdb=" CB ILE Q 190 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 375 not shown) Planarity restraints: 389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 49 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C GLU Q 49 " -0.020 2.00e-02 2.50e+03 pdb=" O GLU Q 49 " 0.007 2.00e-02 2.50e+03 pdb=" N SER Q 50 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR Q 192 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.64e-01 pdb=" N PRO Q 193 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO Q 193 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO Q 193 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Q 138 " 0.012 5.00e-02 4.00e+02 1.80e-02 5.20e-01 pdb=" N PRO Q 139 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO Q 139 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO Q 139 " 0.010 5.00e-02 4.00e+02 ... (remaining 386 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 14 2.47 - 3.08: 1678 3.08 - 3.69: 3351 3.69 - 4.29: 4597 4.29 - 4.90: 7385 Nonbonded interactions: 17025 Sorted by model distance: nonbonded pdb=" O3B GDP Q 401 " pdb="MG MG Q 402 " model vdw 1.865 2.170 nonbonded pdb=" OG SER Q 53 " pdb="MG MG Q 402 " model vdw 1.898 2.170 nonbonded pdb=" O2A GDP Q 401 " pdb=" F1 ALF Q 403 " model vdw 2.254 2.990 nonbonded pdb=" O LYS Q 77 " pdb=" OE1 GLN Q 81 " model vdw 2.286 3.040 nonbonded pdb=" O2B GDP Q 401 " pdb=" F1 ALF Q 403 " model vdw 2.300 2.990 ... (remaining 17020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.600 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.350 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 0.116 2228 Z= 0.274 Angle : 2.021 71.268 3063 Z= 0.707 Chirality : 0.039 0.129 378 Planarity : 0.002 0.020 389 Dihedral : 13.861 113.493 701 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 15.20 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.51), residues: 315 helix: 1.48 (0.43), residues: 167 sheet: -0.52 (0.83), residues: 41 loop : -0.11 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 214 TYR 0.006 0.001 TYR Q 159 PHE 0.006 0.001 PHE Q 313 TRP 0.002 0.001 TRP Q 263 HIS 0.001 0.001 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 2228) covalent geometry : angle 2.02072 ( 3063) hydrogen bonds : bond 0.16626 ( 128) hydrogen bonds : angle 6.00745 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.087 Fit side-chains REVERT: Q 236 ASP cc_start: 0.7794 (t0) cc_final: 0.7553 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.5122 time to fit residues: 16.7826 Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.104592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.086750 restraints weight = 7405.554| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.68 r_work: 0.3554 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2228 Z= 0.131 Angle : 1.339 31.084 3063 Z= 0.495 Chirality : 0.042 0.158 378 Planarity : 0.003 0.018 389 Dihedral : 7.880 93.883 347 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.17 % Allowed : 18.13 % Favored : 80.70 % 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: 1.21 (0.51), residues: 315 helix: 1.73 (0.43), residues: 174 sheet: -0.53 (0.78), residues: 41 loop : -0.16 (0.67), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 92 TYR 0.009 0.001 TYR Q 80 PHE 0.009 0.001 PHE Q 313 TRP 0.005 0.001 TRP Q 263 HIS 0.001 0.001 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2228) covalent geometry : angle 1.33901 ( 3063) hydrogen bonds : bond 0.03200 ( 128) hydrogen bonds : angle 4.52783 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: Q 236 ASP cc_start: 0.8197 (t0) cc_final: 0.7898 (t0) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.4208 time to fit residues: 16.0168 Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 141 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.105508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.087290 restraints weight = 7434.475| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.83 r_work: 0.3548 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2228 Z= 0.113 Angle : 1.331 30.762 3063 Z= 0.486 Chirality : 0.041 0.148 378 Planarity : 0.003 0.018 389 Dihedral : 6.562 60.182 347 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.34 % Allowed : 25.15 % Favored : 72.51 % 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: 1.43 (0.51), residues: 315 helix: 1.91 (0.43), residues: 171 sheet: -0.55 (0.77), residues: 39 loop : 0.06 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 60 TYR 0.012 0.001 TYR Q 325 PHE 0.008 0.001 PHE Q 313 TRP 0.005 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 2228) covalent geometry : angle 1.33096 ( 3063) hydrogen bonds : bond 0.02849 ( 128) hydrogen bonds : angle 4.19606 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: Q 214 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.2355 (mmt180) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.3986 time to fit residues: 14.7819 Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 214 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.105258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087129 restraints weight = 7272.085| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.75 r_work: 0.3549 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2228 Z= 0.121 Angle : 1.335 30.212 3063 Z= 0.489 Chirality : 0.041 0.142 378 Planarity : 0.003 0.023 389 Dihedral : 6.315 64.651 347 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.92 % Allowed : 25.73 % Favored : 71.35 % 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: 1.39 (0.51), residues: 315 helix: 1.88 (0.43), residues: 171 sheet: -0.61 (0.77), residues: 39 loop : 0.06 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 183 TYR 0.013 0.001 TYR Q 235 PHE 0.015 0.001 PHE Q 339 TRP 0.005 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2228) covalent geometry : angle 1.33549 ( 3063) hydrogen bonds : bond 0.02728 ( 128) hydrogen bonds : angle 4.12870 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: Q 214 ARG cc_start: 0.5682 (OUTLIER) cc_final: 0.2426 (mmt180) outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 0.4718 time to fit residues: 17.4546 Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 214 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.105728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.087398 restraints weight = 7250.374| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.78 r_work: 0.3549 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2228 Z= 0.117 Angle : 1.342 29.999 3063 Z= 0.493 Chirality : 0.042 0.141 378 Planarity : 0.003 0.019 389 Dihedral : 6.226 65.346 347 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.68 % Allowed : 25.73 % Favored : 69.59 % 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: 1.37 (0.51), residues: 315 helix: 1.86 (0.43), residues: 171 sheet: -0.74 (0.75), residues: 39 loop : 0.10 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 60 TYR 0.015 0.001 TYR Q 235 PHE 0.009 0.001 PHE Q 339 TRP 0.004 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2228) covalent geometry : angle 1.34156 ( 3063) hydrogen bonds : bond 0.02723 ( 128) hydrogen bonds : angle 4.05315 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: Q 214 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.2245 (mmt180) outliers start: 8 outliers final: 2 residues processed: 38 average time/residue: 0.4065 time to fit residues: 15.9077 Evaluate side-chains 34 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 214 ARG Chi-restraints excluded: chain Q residue 278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.105526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.087207 restraints weight = 7067.679| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.74 r_work: 0.3547 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2228 Z= 0.122 Angle : 1.336 30.089 3063 Z= 0.487 Chirality : 0.042 0.179 378 Planarity : 0.003 0.017 389 Dihedral : 6.287 66.910 347 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.09 % Allowed : 26.90 % Favored : 69.01 % 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: 1.28 (0.50), residues: 315 helix: 1.81 (0.43), residues: 171 sheet: -0.76 (0.73), residues: 39 loop : 0.02 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 181 TYR 0.013 0.001 TYR Q 325 PHE 0.009 0.001 PHE Q 313 TRP 0.004 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2228) covalent geometry : angle 1.33640 ( 3063) hydrogen bonds : bond 0.02722 ( 128) hydrogen bonds : angle 4.08621 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: Q 192 TYR cc_start: 0.8348 (m-10) cc_final: 0.8147 (m-10) REVERT: Q 214 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.2350 (mmt180) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.4574 time to fit residues: 16.4387 Evaluate side-chains 34 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 214 ARG Chi-restraints excluded: chain Q residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.104152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085524 restraints weight = 7400.000| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.75 r_work: 0.3515 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2228 Z= 0.171 Angle : 1.358 30.280 3063 Z= 0.506 Chirality : 0.043 0.153 378 Planarity : 0.003 0.021 389 Dihedral : 6.574 71.998 347 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.75 % Allowed : 29.24 % Favored : 69.01 % 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: 1.48 (0.51), residues: 315 helix: 2.07 (0.44), residues: 163 sheet: -0.89 (0.71), residues: 41 loop : 0.20 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 183 TYR 0.015 0.002 TYR Q 235 PHE 0.011 0.001 PHE Q 313 TRP 0.004 0.001 TRP Q 263 HIS 0.002 0.001 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2228) covalent geometry : angle 1.35803 ( 3063) hydrogen bonds : bond 0.03109 ( 128) hydrogen bonds : angle 4.29908 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.085 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.4426 time to fit residues: 15.8906 Evaluate side-chains 32 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.0470 chunk 15 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.106196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087550 restraints weight = 7249.833| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.80 r_work: 0.3553 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2228 Z= 0.106 Angle : 1.347 29.725 3063 Z= 0.498 Chirality : 0.043 0.199 378 Planarity : 0.003 0.019 389 Dihedral : 6.220 68.876 347 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.92 % Allowed : 29.24 % Favored : 67.84 % 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: 1.63 (0.51), residues: 315 helix: 2.10 (0.43), residues: 163 sheet: -0.94 (0.72), residues: 39 loop : 0.45 (0.68), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 181 TYR 0.013 0.001 TYR Q 325 PHE 0.007 0.001 PHE Q 339 TRP 0.004 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2228) covalent geometry : angle 1.34666 ( 3063) hydrogen bonds : bond 0.02638 ( 128) hydrogen bonds : angle 4.10693 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: Q 214 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.2367 (mmt180) outliers start: 5 outliers final: 0 residues processed: 37 average time/residue: 0.3918 time to fit residues: 14.9344 Evaluate side-chains 32 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 214 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.106240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087396 restraints weight = 7215.370| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.79 r_work: 0.3553 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2228 Z= 0.119 Angle : 1.357 29.841 3063 Z= 0.509 Chirality : 0.043 0.147 378 Planarity : 0.003 0.026 389 Dihedral : 6.203 69.707 347 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.75 % Allowed : 30.99 % Favored : 67.25 % 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: 1.69 (0.52), residues: 315 helix: 2.15 (0.44), residues: 163 sheet: -0.87 (0.72), residues: 39 loop : 0.47 (0.68), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 92 TYR 0.015 0.001 TYR Q 235 PHE 0.007 0.001 PHE Q 313 TRP 0.005 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2228) covalent geometry : angle 1.35698 ( 3063) hydrogen bonds : bond 0.02810 ( 128) hydrogen bonds : angle 4.14997 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: Q 214 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.2474 (mmt180) outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.4655 time to fit residues: 15.7578 Evaluate side-chains 32 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 214 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.105979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087234 restraints weight = 7271.471| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.80 r_work: 0.3549 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2228 Z= 0.111 Angle : 1.340 29.901 3063 Z= 0.492 Chirality : 0.043 0.167 378 Planarity : 0.002 0.019 389 Dihedral : 6.122 68.616 347 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.75 % Allowed : 30.99 % Favored : 67.25 % 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: 1.78 (0.52), residues: 315 helix: 2.20 (0.44), residues: 163 sheet: -0.72 (0.71), residues: 39 loop : 0.51 (0.69), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 60 TYR 0.014 0.001 TYR Q 235 PHE 0.007 0.001 PHE Q 313 TRP 0.005 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2228) covalent geometry : angle 1.33999 ( 3063) hydrogen bonds : bond 0.02567 ( 128) hydrogen bonds : angle 4.05083 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: Q 101 TYR cc_start: 0.7935 (m-10) cc_final: 0.7695 (m-10) REVERT: Q 214 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.2449 (mmt180) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.4083 time to fit residues: 14.2799 Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 214 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 6 optimal weight: 9.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.106831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.087864 restraints weight = 7430.500| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.84 r_work: 0.3564 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2228 Z= 0.104 Angle : 1.359 29.795 3063 Z= 0.502 Chirality : 0.043 0.151 378 Planarity : 0.002 0.020 389 Dihedral : 6.004 67.198 347 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.17 % Allowed : 30.99 % Favored : 67.84 % 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: 1.82 (0.51), residues: 315 helix: 2.21 (0.44), residues: 163 sheet: -0.61 (0.72), residues: 39 loop : 0.52 (0.67), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 92 TYR 0.014 0.001 TYR Q 325 PHE 0.007 0.001 PHE Q 339 TRP 0.004 0.001 TRP Q 263 HIS 0.001 0.000 HIS Q 218 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2228) covalent geometry : angle 1.35918 ( 3063) hydrogen bonds : bond 0.02669 ( 128) hydrogen bonds : angle 4.09637 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1038.45 seconds wall clock time: 18 minutes 27.10 seconds (1107.10 seconds total)