Starting phenix.real_space_refine on Fri Aug 22 14:14:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uf7_42185/08_2025/8uf7_42185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uf7_42185/08_2025/8uf7_42185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uf7_42185/08_2025/8uf7_42185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uf7_42185/08_2025/8uf7_42185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uf7_42185/08_2025/8uf7_42185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uf7_42185/08_2025/8uf7_42185.map" } resolution = 3.2 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2449 2.51 5 N 669 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3927 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1651 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1620 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "C" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 656 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 76} Time building chain proxies: 1.15, per 1000 atoms: 0.29 Number of scatterers: 3927 At special positions: 0 Unit cell: (56.212, 62.698, 112.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 786 8.00 N 669 7.00 C 2449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 138 " 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: 0.32 Conformation dependent library (CDL) restraints added in 163.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 5.1% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 122 through 129 removed outlier: 3.538A pdb=" N GLY A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.941A pdb=" N GLN B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.508A pdb=" N MET A 11 " --> pdb=" O GLU A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.563A pdb=" N MET A 21 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.699A pdb=" N LEU A 47 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN A 38 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 119 removed outlier: 3.611A pdb=" N PHE A 136 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 134 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 178 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 139 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.638A pdb=" N LYS A 208 " --> pdb=" O CYS A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 237 removed outlier: 3.513A pdb=" N LEU B 233 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 286 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.760A pdb=" N THR B 265 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 253 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP B 251 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR B 265 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 249 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 344 through 345 removed outlier: 3.531A pdb=" N LEU B 345 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 400 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR B 397 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA B 389 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 399 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 375 Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.648A pdb=" N GLN C 136 " --> pdb=" O CYS C 126 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 183 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: 0.65 Time building geometry restraints manager: 0.45 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: 1266 1.34 - 1.46: 966 1.46 - 1.58: 1760 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 4023 Sorted by residual: bond pdb=" C SER A 43 " pdb=" N SER A 44 " ideal model delta sigma weight residual 1.339 1.258 0.082 5.57e-02 3.22e+02 2.15e+00 bond pdb=" CB PRO B 344 " pdb=" CG PRO B 344 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.38e+00 bond pdb=" CG LEU B 260 " pdb=" CD1 LEU B 260 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CG LEU B 296 " pdb=" CD1 LEU B 296 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CB VAL B 402 " pdb=" CG2 VAL B 402 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 ... (remaining 4018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 5278 1.56 - 3.13: 166 3.13 - 4.69: 28 4.69 - 6.25: 6 6.25 - 7.81: 3 Bond angle restraints: 5481 Sorted by residual: angle pdb=" N SER A 27 " pdb=" CA SER A 27 " pdb=" CB SER A 27 " ideal model delta sigma weight residual 114.17 110.12 4.05 1.14e+00 7.69e-01 1.26e+01 angle pdb=" C LYS B 426 " pdb=" N VAL B 427 " pdb=" CA VAL B 427 " ideal model delta sigma weight residual 121.97 126.81 -4.84 1.80e+00 3.09e-01 7.22e+00 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 113.18 106.89 6.29 2.37e+00 1.78e-01 7.04e+00 angle pdb=" C ALA B 335 " pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 121.54 125.88 -4.34 1.91e+00 2.74e-01 5.17e+00 angle pdb=" CA LEU B 235 " pdb=" CB LEU B 235 " pdb=" CG LEU B 235 " ideal model delta sigma weight residual 116.30 124.11 -7.81 3.50e+00 8.16e-02 4.98e+00 ... (remaining 5476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1975 16.50 - 33.01: 305 33.01 - 49.51: 101 49.51 - 66.01: 26 66.01 - 82.51: 6 Dihedral angle restraints: 2413 sinusoidal: 926 harmonic: 1487 Sorted by residual: dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 143 " pdb=" CB CYS C 143 " ideal model delta sinusoidal sigma weight residual -86.00 -43.06 -42.94 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 126 " pdb=" CB CYS C 126 " ideal model delta sinusoidal sigma weight residual -86.00 -44.98 -41.02 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA TYR A 37 " pdb=" C TYR A 37 " pdb=" N GLN A 38 " pdb=" CA GLN A 38 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 322 0.028 - 0.056: 180 0.056 - 0.085: 56 0.085 - 0.113: 44 0.113 - 0.141: 11 Chirality restraints: 613 Sorted by residual: chirality pdb=" CG LEU B 345 " pdb=" CB LEU B 345 " pdb=" CD1 LEU B 345 " pdb=" CD2 LEU B 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 10 " pdb=" N ILE A 10 " pdb=" C ILE A 10 " pdb=" CB ILE A 10 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 610 not shown) Planarity restraints: 701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 343 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO B 344 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 375 " 0.017 2.00e-02 2.50e+03 1.49e-02 5.56e+00 pdb=" CG TRP B 375 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 375 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 375 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 375 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 375 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 375 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 375 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 375 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 367 " 0.036 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 368 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " 0.027 5.00e-02 4.00e+02 ... (remaining 698 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 483 2.74 - 3.28: 3907 3.28 - 3.82: 6653 3.82 - 4.36: 7630 4.36 - 4.90: 12989 Nonbonded interactions: 31662 Sorted by model distance: nonbonded pdb=" NH1 ARG A 156 " pdb=" OD1 ASN A 158 " model vdw 2.204 3.120 nonbonded pdb=" NH2 ARG B 282 " pdb=" OD2 ASP B 305 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" OE1 GLN A 90 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 250 " pdb=" NH2 ARG C 90 " model vdw 2.221 3.120 nonbonded pdb=" NZ LYS A 40 " pdb=" O GLU A 82 " model vdw 2.225 3.120 ... (remaining 31657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.100 Set stop_for_unknowns flag: 0.010 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 4030 Z= 0.210 Angle : 0.696 7.814 5495 Z= 0.356 Chirality : 0.045 0.141 613 Planarity : 0.006 0.063 701 Dihedral : 18.207 82.515 1442 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.80 % Favored : 86.61 % Rotamer: Outliers : 0.89 % Allowed : 44.30 % Favored : 54.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.37), residues: 508 helix: -0.24 (1.21), residues: 20 sheet: -1.48 (0.41), residues: 160 loop : -1.60 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.012 0.002 TYR B 366 PHE 0.008 0.001 PHE A 63 TRP 0.040 0.003 TRP B 375 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 4023) covalent geometry : angle 0.69512 ( 5481) SS BOND : bond 0.00350 ( 7) SS BOND : angle 0.94217 ( 14) hydrogen bonds : bond 0.30517 ( 77) hydrogen bonds : angle 12.08692 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.158 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.0570 time to fit residues: 6.1917 Evaluate side-chains 80 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.0870 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.182213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164758 restraints weight = 5514.126| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.09 r_work: 0.4029 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4030 Z= 0.133 Angle : 0.658 7.240 5495 Z= 0.334 Chirality : 0.043 0.136 613 Planarity : 0.005 0.052 701 Dihedral : 5.534 51.971 562 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.02 % Favored : 88.39 % Rotamer: Outliers : 6.04 % Allowed : 36.69 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.37), residues: 508 helix: 0.38 (1.23), residues: 22 sheet: -1.36 (0.42), residues: 150 loop : -1.50 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.012 0.001 TYR B 248 PHE 0.005 0.001 PHE A 63 TRP 0.022 0.002 TRP B 375 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4023) covalent geometry : angle 0.65756 ( 5481) SS BOND : bond 0.00247 ( 7) SS BOND : angle 0.79690 ( 14) hydrogen bonds : bond 0.03989 ( 77) hydrogen bonds : angle 8.12117 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.154 Fit side-chains REVERT: A 38 GLN cc_start: 0.7430 (pt0) cc_final: 0.7058 (pt0) REVERT: B 232 SER cc_start: 0.4769 (OUTLIER) cc_final: 0.4286 (m) outliers start: 27 outliers final: 19 residues processed: 93 average time/residue: 0.0472 time to fit residues: 5.9797 Evaluate side-chains 96 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 7 optimal weight: 0.8980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161641 restraints weight = 5541.439| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.07 r_work: 0.3995 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 4030 Z= 0.201 Angle : 0.683 6.978 5495 Z= 0.345 Chirality : 0.045 0.136 613 Planarity : 0.005 0.055 701 Dihedral : 5.775 55.487 562 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.20 % Favored : 87.20 % Rotamer: Outliers : 8.50 % Allowed : 35.79 % Favored : 55.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.37), residues: 508 helix: 0.10 (1.17), residues: 22 sheet: -1.32 (0.41), residues: 159 loop : -1.60 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 90 TYR 0.013 0.002 TYR B 248 PHE 0.008 0.001 PHE A 63 TRP 0.024 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 4023) covalent geometry : angle 0.68235 ( 5481) SS BOND : bond 0.00283 ( 7) SS BOND : angle 0.88346 ( 14) hydrogen bonds : bond 0.03790 ( 77) hydrogen bonds : angle 7.67854 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.148 Fit side-chains REVERT: A 38 GLN cc_start: 0.7867 (pt0) cc_final: 0.7414 (pt0) REVERT: A 48 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.6145 (m100) REVERT: B 232 SER cc_start: 0.5004 (OUTLIER) cc_final: 0.4554 (m) outliers start: 38 outliers final: 27 residues processed: 103 average time/residue: 0.0530 time to fit residues: 7.3514 Evaluate side-chains 106 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 12 optimal weight: 0.0670 chunk 39 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 31 optimal weight: 0.5980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.182764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165028 restraints weight = 5414.854| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 3.11 r_work: 0.4028 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4030 Z= 0.124 Angle : 0.630 6.716 5495 Z= 0.315 Chirality : 0.043 0.130 613 Planarity : 0.005 0.054 701 Dihedral : 5.531 59.243 562 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.43 % Favored : 88.98 % Rotamer: Outliers : 7.83 % Allowed : 35.35 % Favored : 56.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.37), residues: 508 helix: 0.10 (1.19), residues: 22 sheet: -1.33 (0.43), residues: 150 loop : -1.57 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 90 TYR 0.009 0.001 TYR B 248 PHE 0.006 0.001 PHE A 140 TRP 0.019 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4023) covalent geometry : angle 0.62998 ( 5481) SS BOND : bond 0.00200 ( 7) SS BOND : angle 0.70721 ( 14) hydrogen bonds : bond 0.03045 ( 77) hydrogen bonds : angle 7.06534 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.145 Fit side-chains REVERT: A 38 GLN cc_start: 0.7821 (pt0) cc_final: 0.7466 (pt0) REVERT: B 232 SER cc_start: 0.4848 (OUTLIER) cc_final: 0.4224 (m) outliers start: 35 outliers final: 28 residues processed: 101 average time/residue: 0.0443 time to fit residues: 6.0208 Evaluate side-chains 104 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 4 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.181128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163419 restraints weight = 5458.310| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.11 r_work: 0.4012 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 4030 Z= 0.153 Angle : 0.643 7.309 5495 Z= 0.322 Chirality : 0.044 0.134 613 Planarity : 0.005 0.055 701 Dihedral : 5.615 59.020 562 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.81 % Favored : 87.60 % Rotamer: Outliers : 8.50 % Allowed : 33.56 % Favored : 57.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.37), residues: 508 helix: -0.02 (1.16), residues: 22 sheet: -1.34 (0.42), residues: 150 loop : -1.56 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.010 0.001 TYR B 248 PHE 0.007 0.001 PHE A 140 TRP 0.023 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4023) covalent geometry : angle 0.64264 ( 5481) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.67520 ( 14) hydrogen bonds : bond 0.03019 ( 77) hydrogen bonds : angle 6.92942 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.125 Fit side-chains REVERT: A 38 GLN cc_start: 0.7953 (pt0) cc_final: 0.7682 (pt0) REVERT: A 48 TRP cc_start: 0.6413 (OUTLIER) cc_final: 0.6001 (m100) REVERT: B 376 ASN cc_start: 0.7736 (m-40) cc_final: 0.7488 (m-40) outliers start: 38 outliers final: 29 residues processed: 101 average time/residue: 0.0389 time to fit residues: 5.4699 Evaluate side-chains 108 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.179598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162271 restraints weight = 5520.490| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.08 r_work: 0.4001 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 4030 Z= 0.187 Angle : 0.668 7.359 5495 Z= 0.336 Chirality : 0.045 0.136 613 Planarity : 0.005 0.056 701 Dihedral : 5.721 56.390 562 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.20 % Favored : 87.20 % Rotamer: Outliers : 9.17 % Allowed : 33.11 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.37), residues: 508 helix: -0.23 (1.13), residues: 22 sheet: -1.20 (0.42), residues: 159 loop : -1.63 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 90 TYR 0.010 0.002 TYR B 248 PHE 0.008 0.001 PHE A 63 TRP 0.026 0.002 TRP B 375 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 4023) covalent geometry : angle 0.66769 ( 5481) SS BOND : bond 0.00245 ( 7) SS BOND : angle 0.70894 ( 14) hydrogen bonds : bond 0.03081 ( 77) hydrogen bonds : angle 6.80946 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.129 Fit side-chains REVERT: A 38 GLN cc_start: 0.7975 (pt0) cc_final: 0.7632 (pt0) REVERT: A 48 TRP cc_start: 0.6451 (OUTLIER) cc_final: 0.6022 (m100) REVERT: A 91 LEU cc_start: 0.7401 (tp) cc_final: 0.6937 (tt) outliers start: 41 outliers final: 31 residues processed: 108 average time/residue: 0.0462 time to fit residues: 6.7454 Evaluate side-chains 111 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.180027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162607 restraints weight = 5555.956| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.08 r_work: 0.4001 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 4030 Z= 0.177 Angle : 0.672 6.966 5495 Z= 0.339 Chirality : 0.044 0.134 613 Planarity : 0.005 0.057 701 Dihedral : 5.688 54.505 562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.40 % Favored : 87.01 % Rotamer: Outliers : 8.50 % Allowed : 33.78 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.37), residues: 508 helix: -0.24 (1.15), residues: 22 sheet: -1.23 (0.42), residues: 159 loop : -1.64 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.013 0.002 TYR B 248 PHE 0.008 0.001 PHE A 140 TRP 0.028 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4023) covalent geometry : angle 0.67006 ( 5481) SS BOND : bond 0.00247 ( 7) SS BOND : angle 1.27188 ( 14) hydrogen bonds : bond 0.03022 ( 77) hydrogen bonds : angle 6.77567 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.092 Fit side-chains REVERT: A 38 GLN cc_start: 0.7990 (pt0) cc_final: 0.7683 (pt0) REVERT: A 48 TRP cc_start: 0.6470 (OUTLIER) cc_final: 0.5992 (m100) REVERT: A 91 LEU cc_start: 0.7377 (tp) cc_final: 0.6968 (tt) REVERT: B 232 SER cc_start: 0.5040 (OUTLIER) cc_final: 0.4403 (m) outliers start: 38 outliers final: 31 residues processed: 105 average time/residue: 0.0421 time to fit residues: 6.2065 Evaluate side-chains 110 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 10 optimal weight: 0.0070 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.181248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.164099 restraints weight = 5463.525| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.03 r_work: 0.4021 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4030 Z= 0.154 Angle : 0.657 7.625 5495 Z= 0.330 Chirality : 0.044 0.132 613 Planarity : 0.005 0.057 701 Dihedral : 5.558 51.932 562 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.81 % Favored : 87.60 % Rotamer: Outliers : 8.28 % Allowed : 34.23 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.37), residues: 508 helix: -0.25 (1.14), residues: 22 sheet: -1.24 (0.42), residues: 159 loop : -1.64 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.012 0.001 TYR B 248 PHE 0.008 0.001 PHE A 140 TRP 0.028 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4023) covalent geometry : angle 0.65443 ( 5481) SS BOND : bond 0.00179 ( 7) SS BOND : angle 1.23212 ( 14) hydrogen bonds : bond 0.02860 ( 77) hydrogen bonds : angle 6.62688 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.145 Fit side-chains REVERT: A 38 GLN cc_start: 0.7951 (pt0) cc_final: 0.7584 (pt0) REVERT: A 48 TRP cc_start: 0.6359 (OUTLIER) cc_final: 0.5872 (m100) REVERT: A 91 LEU cc_start: 0.7412 (tp) cc_final: 0.7036 (tt) REVERT: B 232 SER cc_start: 0.5049 (OUTLIER) cc_final: 0.4429 (m) outliers start: 37 outliers final: 31 residues processed: 106 average time/residue: 0.0401 time to fit residues: 5.9418 Evaluate side-chains 110 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0470 chunk 21 optimal weight: 0.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.182981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.165586 restraints weight = 5553.128| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.09 r_work: 0.4038 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4030 Z= 0.125 Angle : 0.635 7.692 5495 Z= 0.318 Chirality : 0.043 0.129 613 Planarity : 0.005 0.057 701 Dihedral : 5.318 48.456 562 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.81 % Favored : 87.60 % Rotamer: Outliers : 7.38 % Allowed : 35.12 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.37), residues: 508 helix: -0.18 (1.13), residues: 22 sheet: -1.18 (0.42), residues: 161 loop : -1.62 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.009 0.001 TYR B 248 PHE 0.008 0.001 PHE A 140 TRP 0.024 0.002 TRP B 375 HIS 0.002 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4023) covalent geometry : angle 0.63301 ( 5481) SS BOND : bond 0.00168 ( 7) SS BOND : angle 1.11697 ( 14) hydrogen bonds : bond 0.02760 ( 77) hydrogen bonds : angle 6.37457 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.148 Fit side-chains REVERT: A 27 SER cc_start: 0.6213 (OUTLIER) cc_final: 0.5786 (p) REVERT: A 38 GLN cc_start: 0.7877 (pt0) cc_final: 0.7513 (pt0) REVERT: A 48 TRP cc_start: 0.6262 (OUTLIER) cc_final: 0.5770 (m100) REVERT: A 91 LEU cc_start: 0.7360 (tp) cc_final: 0.6991 (tt) REVERT: B 232 SER cc_start: 0.4998 (OUTLIER) cc_final: 0.4388 (m) outliers start: 33 outliers final: 27 residues processed: 100 average time/residue: 0.0413 time to fit residues: 5.7951 Evaluate side-chains 105 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.181447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162465 restraints weight = 5516.363| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.38 r_work: 0.3984 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 4030 Z= 0.194 Angle : 0.688 7.685 5495 Z= 0.347 Chirality : 0.045 0.136 613 Planarity : 0.005 0.056 701 Dihedral : 5.607 46.795 562 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.01 % Favored : 87.40 % Rotamer: Outliers : 7.61 % Allowed : 34.90 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.37), residues: 508 helix: -0.31 (1.10), residues: 22 sheet: -1.34 (0.42), residues: 159 loop : -1.67 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 115 TYR 0.012 0.002 TYR B 248 PHE 0.008 0.001 PHE A 140 TRP 0.035 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 4023) covalent geometry : angle 0.68644 ( 5481) SS BOND : bond 0.00259 ( 7) SS BOND : angle 1.22706 ( 14) hydrogen bonds : bond 0.03061 ( 77) hydrogen bonds : angle 6.66081 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.143 Fit side-chains REVERT: A 27 SER cc_start: 0.6238 (OUTLIER) cc_final: 0.5777 (p) REVERT: A 38 GLN cc_start: 0.8001 (pt0) cc_final: 0.7611 (pt0) REVERT: A 48 TRP cc_start: 0.6442 (OUTLIER) cc_final: 0.5898 (m100) REVERT: B 232 SER cc_start: 0.5034 (OUTLIER) cc_final: 0.4433 (m) outliers start: 34 outliers final: 27 residues processed: 103 average time/residue: 0.0435 time to fit residues: 6.2059 Evaluate side-chains 106 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.183027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.164087 restraints weight = 5463.187| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.38 r_work: 0.4003 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4030 Z= 0.149 Angle : 0.662 7.261 5495 Z= 0.332 Chirality : 0.044 0.133 613 Planarity : 0.005 0.057 701 Dihedral : 4.836 16.776 560 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.01 % Favored : 87.40 % Rotamer: Outliers : 6.71 % Allowed : 35.57 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.37), residues: 508 helix: -0.17 (1.11), residues: 22 sheet: -1.33 (0.42), residues: 160 loop : -1.64 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.010 0.001 TYR B 248 PHE 0.008 0.001 PHE A 140 TRP 0.031 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4023) covalent geometry : angle 0.66005 ( 5481) SS BOND : bond 0.00207 ( 7) SS BOND : angle 1.16123 ( 14) hydrogen bonds : bond 0.02819 ( 77) hydrogen bonds : angle 6.48246 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.75 seconds wall clock time: 18 minutes 51.24 seconds (1131.24 seconds total)