Starting phenix.real_space_refine on Fri May 9 21:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uf7_42185/05_2025/8uf7_42185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uf7_42185/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uf7_42185/05_2025/8uf7_42185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uf7_42185/05_2025/8uf7_42185.map" model { file = "/net/cci-nas-00/data/ceres_data/8uf7_42185/05_2025/8uf7_42185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uf7_42185/05_2025/8uf7_42185.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.72, per 1000 atoms: 0.69 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: 0.98 Conformation dependent library (CDL) restraints added in 438.6 milliseconds 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: 0.40 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: 0.98 Time building geometry restraints manager: 1.16 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: 0.850 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.003 TRP B 375 HIS 0.005 0.001 HIS C 104 PHE 0.008 0.001 PHE A 63 TYR 0.012 0.002 TYR B 366 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.30517 ( 77) hydrogen bonds : angle 12.08692 ( 183) SS BOND : bond 0.00350 ( 7) SS BOND : angle 0.94217 ( 14) covalent geometry : bond 0.00481 ( 4023) covalent geometry : angle 0.69512 ( 5481) *********************** 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 : 0.372 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.1288 time to fit residues: 13.8343 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 : 0.385 ------------------------------------------------------------------------------- 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 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.180279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163140 restraints weight = 5430.560| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.03 r_work: 0.4011 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 4030 Z= 0.171 Angle : 0.683 7.230 5495 Z= 0.346 Chirality : 0.044 0.137 613 Planarity : 0.006 0.054 701 Dihedral : 5.730 52.667 562 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.01 % Favored : 87.40 % Rotamer: Outliers : 6.04 % Allowed : 37.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.37), residues: 508 helix: 0.38 (1.22), residues: 22 sheet: -1.37 (0.41), residues: 159 loop : -1.56 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 375 HIS 0.004 0.001 HIS A 72 PHE 0.008 0.001 PHE A 63 TYR 0.013 0.002 TYR B 248 ARG 0.005 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 77) hydrogen bonds : angle 8.22380 ( 183) SS BOND : bond 0.00261 ( 7) SS BOND : angle 0.88707 ( 14) covalent geometry : bond 0.00398 ( 4023) covalent geometry : angle 0.68201 ( 5481) *********************** 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 107 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.502 Fit side-chains REVERT: A 38 GLN cc_start: 0.7667 (pt0) cc_final: 0.7283 (pt0) REVERT: B 232 SER cc_start: 0.4883 (OUTLIER) cc_final: 0.4400 (m) outliers start: 27 outliers final: 18 residues processed: 94 average time/residue: 0.1197 time to fit residues: 15.1082 Evaluate side-chains 97 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 118 ILE Chi-restraints excluded: chain A residue 208 LYS 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 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 359 LEU 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 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 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.180145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163003 restraints weight = 5507.808| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.03 r_work: 0.4008 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 4030 Z= 0.161 Angle : 0.657 6.509 5495 Z= 0.331 Chirality : 0.044 0.134 613 Planarity : 0.005 0.055 701 Dihedral : 5.663 55.947 562 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.60 % Favored : 86.81 % Rotamer: Outliers : 8.28 % Allowed : 35.12 % Favored : 56.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.37), residues: 508 helix: 0.16 (1.19), residues: 22 sheet: -1.30 (0.41), residues: 160 loop : -1.56 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.007 0.001 PHE A 63 TYR 0.013 0.001 TYR B 248 ARG 0.005 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 77) hydrogen bonds : angle 7.49312 ( 183) SS BOND : bond 0.00260 ( 7) SS BOND : angle 0.81894 ( 14) covalent geometry : bond 0.00376 ( 4023) covalent geometry : angle 0.65655 ( 5481) *********************** 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: 37 poor density : 79 time to evaluate : 0.403 Fit side-chains REVERT: A 38 GLN cc_start: 0.7827 (pt0) cc_final: 0.7417 (pt0) REVERT: B 232 SER cc_start: 0.4965 (OUTLIER) cc_final: 0.4308 (m) outliers start: 37 outliers final: 27 residues processed: 107 average time/residue: 0.1124 time to fit residues: 16.2653 Evaluate side-chains 104 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 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 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 332 VAL Chi-restraints excluded: chain B residue 337 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 Chi-restraints excluded: chain C residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 26 optimal weight: 0.4980 chunk 45 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.0020 overall best weight: 0.2434 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.182871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165463 restraints weight = 5425.011| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.05 r_work: 0.4037 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4030 Z= 0.123 Angle : 0.632 7.494 5495 Z= 0.316 Chirality : 0.043 0.131 613 Planarity : 0.005 0.055 701 Dihedral : 5.512 58.878 562 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.63 % Favored : 88.78 % Rotamer: Outliers : 7.61 % Allowed : 35.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.37), residues: 508 helix: 0.13 (1.20), residues: 22 sheet: -1.33 (0.42), residues: 150 loop : -1.53 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.006 0.001 PHE A 140 TYR 0.010 0.001 TYR B 248 ARG 0.005 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 77) hydrogen bonds : angle 6.98186 ( 183) SS BOND : bond 0.00181 ( 7) SS BOND : angle 0.71169 ( 14) covalent geometry : bond 0.00293 ( 4023) covalent geometry : angle 0.63194 ( 5481) *********************** 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 113 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.428 Fit side-chains REVERT: A 38 GLN cc_start: 0.7816 (pt0) cc_final: 0.7446 (pt0) outliers start: 34 outliers final: 28 residues processed: 102 average time/residue: 0.1175 time to fit residues: 15.9015 Evaluate side-chains 105 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 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 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 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 24 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 = 0.4283 r_free = 0.4283 target = 0.177472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.158170 restraints weight = 5617.995| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.43 r_work: 0.3948 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 4030 Z= 0.270 Angle : 0.740 7.186 5495 Z= 0.374 Chirality : 0.047 0.139 613 Planarity : 0.005 0.057 701 Dihedral : 6.143 59.517 562 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.60 % Favored : 86.81 % Rotamer: Outliers : 9.40 % Allowed : 32.21 % Favored : 58.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.37), residues: 508 helix: -0.42 (1.11), residues: 22 sheet: -1.34 (0.41), residues: 159 loop : -1.67 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 375 HIS 0.005 0.001 HIS C 104 PHE 0.011 0.002 PHE A 63 TYR 0.015 0.002 TYR A 50 ARG 0.004 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 77) hydrogen bonds : angle 7.19658 ( 183) SS BOND : bond 0.00348 ( 7) SS BOND : angle 0.94713 ( 14) covalent geometry : bond 0.00621 ( 4023) covalent geometry : angle 0.73896 ( 5481) *********************** 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 123 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.395 Fit side-chains REVERT: A 38 GLN cc_start: 0.7976 (pt0) cc_final: 0.7594 (pt0) REVERT: A 48 TRP cc_start: 0.6548 (OUTLIER) cc_final: 0.6061 (m100) REVERT: A 91 LEU cc_start: 0.7521 (tp) cc_final: 0.7126 (tt) REVERT: B 232 SER cc_start: 0.5041 (OUTLIER) cc_final: 0.4611 (m) REVERT: B 392 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6828 (pt0) outliers start: 42 outliers final: 32 residues processed: 109 average time/residue: 0.0983 time to fit residues: 14.8784 Evaluate side-chains 114 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 124 GLU 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 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 374 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLN 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 82 SER Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 99 ILE 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 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159377 restraints weight = 5516.129| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.06 r_work: 0.3972 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 4030 Z= 0.227 Angle : 0.711 6.870 5495 Z= 0.359 Chirality : 0.047 0.281 613 Planarity : 0.005 0.059 701 Dihedral : 5.990 55.469 562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.20 % Favored : 87.20 % Rotamer: Outliers : 8.72 % Allowed : 33.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.36), residues: 508 helix: -0.60 (1.11), residues: 22 sheet: -1.39 (0.41), residues: 159 loop : -1.78 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 375 HIS 0.005 0.001 HIS C 104 PHE 0.012 0.002 PHE A 63 TYR 0.013 0.002 TYR B 248 ARG 0.002 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 77) hydrogen bonds : angle 7.06296 ( 183) SS BOND : bond 0.00305 ( 7) SS BOND : angle 0.78243 ( 14) covalent geometry : bond 0.00521 ( 4023) covalent geometry : angle 0.71099 ( 5481) *********************** 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 120 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.341 Fit side-chains REVERT: A 26 SER cc_start: 0.4714 (OUTLIER) cc_final: 0.3689 (p) REVERT: A 38 GLN cc_start: 0.7956 (pt0) cc_final: 0.7564 (pt0) REVERT: A 48 TRP cc_start: 0.6565 (OUTLIER) cc_final: 0.6068 (m100) REVERT: A 91 LEU cc_start: 0.7493 (tp) cc_final: 0.7094 (tt) REVERT: B 232 SER cc_start: 0.5061 (OUTLIER) cc_final: 0.4395 (m) outliers start: 39 outliers final: 29 residues processed: 110 average time/residue: 0.1044 time to fit residues: 15.7443 Evaluate side-chains 110 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 26 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 118 ILE 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 273 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.160361 restraints weight = 5471.210| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.06 r_work: 0.3982 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 4030 Z= 0.195 Angle : 0.705 7.059 5495 Z= 0.355 Chirality : 0.046 0.211 613 Planarity : 0.005 0.059 701 Dihedral : 5.862 52.876 562 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.20 % Favored : 87.20 % Rotamer: Outliers : 8.95 % Allowed : 33.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.37), residues: 508 helix: -0.60 (1.13), residues: 22 sheet: -1.38 (0.42), residues: 159 loop : -1.77 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.010 0.001 PHE A 140 TYR 0.012 0.002 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 77) hydrogen bonds : angle 6.95991 ( 183) SS BOND : bond 0.00252 ( 7) SS BOND : angle 1.29270 ( 14) covalent geometry : bond 0.00454 ( 4023) covalent geometry : angle 0.70269 ( 5481) *********************** 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 123 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.449 Fit side-chains REVERT: A 38 GLN cc_start: 0.7982 (pt0) cc_final: 0.7636 (pt0) REVERT: A 48 TRP cc_start: 0.6538 (OUTLIER) cc_final: 0.6015 (m100) REVERT: A 91 LEU cc_start: 0.7462 (tp) cc_final: 0.7096 (tt) REVERT: B 232 SER cc_start: 0.5057 (OUTLIER) cc_final: 0.4406 (m) REVERT: C 140 ILE cc_start: 0.4548 (OUTLIER) cc_final: 0.4084 (tp) outliers start: 40 outliers final: 30 residues processed: 111 average time/residue: 0.1180 time to fit residues: 17.7809 Evaluate side-chains 114 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain B residue 273 THR 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 140 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.177448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160038 restraints weight = 5489.012| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.09 r_work: 0.3975 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 4030 Z= 0.204 Angle : 0.714 7.185 5495 Z= 0.361 Chirality : 0.047 0.266 613 Planarity : 0.005 0.060 701 Dihedral : 5.858 50.278 562 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.60 % Favored : 86.81 % Rotamer: Outliers : 8.50 % Allowed : 34.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.36), residues: 508 helix: -0.70 (1.12), residues: 22 sheet: -1.41 (0.41), residues: 159 loop : -1.80 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.010 0.002 PHE A 140 TYR 0.012 0.002 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 77) hydrogen bonds : angle 6.94806 ( 183) SS BOND : bond 0.00242 ( 7) SS BOND : angle 1.27111 ( 14) covalent geometry : bond 0.00473 ( 4023) covalent geometry : angle 0.71200 ( 5481) *********************** 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 120 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.469 Fit side-chains REVERT: A 26 SER cc_start: 0.4769 (OUTLIER) cc_final: 0.3648 (p) REVERT: A 38 GLN cc_start: 0.7971 (pt0) cc_final: 0.7606 (pt0) REVERT: A 48 TRP cc_start: 0.6538 (OUTLIER) cc_final: 0.5995 (m100) REVERT: B 232 SER cc_start: 0.5072 (OUTLIER) cc_final: 0.4432 (m) REVERT: B 376 ASN cc_start: 0.7771 (m-40) cc_final: 0.7568 (m-40) REVERT: C 140 ILE cc_start: 0.4510 (OUTLIER) cc_final: 0.3997 (tp) outliers start: 38 outliers final: 31 residues processed: 108 average time/residue: 0.1026 time to fit residues: 15.2926 Evaluate side-chains 116 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 26 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 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 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 140 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 chunk 21 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163267 restraints weight = 5499.006| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.10 r_work: 0.4020 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4030 Z= 0.131 Angle : 0.661 7.240 5495 Z= 0.331 Chirality : 0.045 0.181 613 Planarity : 0.005 0.060 701 Dihedral : 5.497 47.315 562 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.02 % Favored : 88.39 % Rotamer: Outliers : 7.83 % Allowed : 35.57 % Favored : 56.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.37), residues: 508 helix: -0.37 (1.15), residues: 22 sheet: -1.37 (0.42), residues: 160 loop : -1.76 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.008 0.001 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 77) hydrogen bonds : angle 6.51116 ( 183) SS BOND : bond 0.00166 ( 7) SS BOND : angle 1.12335 ( 14) covalent geometry : bond 0.00312 ( 4023) covalent geometry : angle 0.65920 ( 5481) *********************** 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 112 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.414 Fit side-chains REVERT: A 21 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5311 (ttm) REVERT: A 26 SER cc_start: 0.4590 (OUTLIER) cc_final: 0.3264 (p) REVERT: A 38 GLN cc_start: 0.7838 (pt0) cc_final: 0.7474 (pt0) REVERT: A 48 TRP cc_start: 0.6393 (OUTLIER) cc_final: 0.5850 (m100) REVERT: C 140 ILE cc_start: 0.4278 (OUTLIER) cc_final: 0.3823 (tp) outliers start: 35 outliers final: 26 residues processed: 101 average time/residue: 0.1116 time to fit residues: 15.1937 Evaluate side-chains 107 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 21 MET Chi-restraints excluded: chain A residue 26 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 243 THR 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 358 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 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 Chi-restraints excluded: chain C residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 4 optimal weight: 0.0670 chunk 37 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 41 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 overall best weight: 0.0490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.189879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.171630 restraints weight = 5529.093| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 3.24 r_work: 0.4103 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4030 Z= 0.107 Angle : 0.629 8.033 5495 Z= 0.313 Chirality : 0.043 0.130 613 Planarity : 0.005 0.060 701 Dihedral : 4.391 17.542 560 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.46 % Favored : 91.14 % Rotamer: Outliers : 5.15 % Allowed : 37.81 % Favored : 57.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.37), residues: 508 helix: -0.15 (1.15), residues: 22 sheet: -1.24 (0.42), residues: 164 loop : -1.72 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 409 HIS 0.005 0.001 HIS A 35 PHE 0.011 0.001 PHE A 119 TYR 0.009 0.001 TYR C 93 ARG 0.003 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 77) hydrogen bonds : angle 5.87040 ( 183) SS BOND : bond 0.00211 ( 7) SS BOND : angle 1.09876 ( 14) covalent geometry : bond 0.00250 ( 4023) covalent geometry : angle 0.62717 ( 5481) ********************** 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 91 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.380 Fit side-chains REVERT: A 21 MET cc_start: 0.5986 (mtm) cc_final: 0.5595 (ttm) REVERT: A 26 SER cc_start: 0.4351 (OUTLIER) cc_final: 0.2384 (t) REVERT: A 38 GLN cc_start: 0.7390 (pt0) cc_final: 0.7170 (pt0) REVERT: A 48 TRP cc_start: 0.6250 (OUTLIER) cc_final: 0.5646 (m100) REVERT: A 175 SER cc_start: 0.7781 (m) cc_final: 0.7150 (p) REVERT: B 298 MET cc_start: 0.6498 (mtm) cc_final: 0.5472 (mtm) REVERT: C 140 ILE cc_start: 0.4263 (OUTLIER) cc_final: 0.3858 (tp) outliers start: 23 outliers final: 16 residues processed: 84 average time/residue: 0.1062 time to fit residues: 12.1317 Evaluate side-chains 86 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 26 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 177 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE 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 99 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.182785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.164694 restraints weight = 5336.444| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.28 r_work: 0.3997 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 4030 Z= 0.235 Angle : 0.734 7.258 5495 Z= 0.370 Chirality : 0.048 0.269 613 Planarity : 0.005 0.058 701 Dihedral : 5.102 19.970 560 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.83 % Favored : 88.58 % Rotamer: Outliers : 6.04 % Allowed : 38.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.37), residues: 508 helix: -0.64 (1.08), residues: 22 sheet: -1.30 (0.42), residues: 160 loop : -1.62 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 375 HIS 0.007 0.002 HIS A 72 PHE 0.013 0.002 PHE A 140 TYR 0.013 0.002 TYR A 50 ARG 0.003 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 77) hydrogen bonds : angle 6.44451 ( 183) SS BOND : bond 0.00276 ( 7) SS BOND : angle 1.20865 ( 14) covalent geometry : bond 0.00549 ( 4023) covalent geometry : angle 0.73210 ( 5481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2133.75 seconds wall clock time: 37 minutes 49.22 seconds (2269.22 seconds total)