Starting phenix.real_space_refine on Sun Apr 27 00:13:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uf7_42185/04_2025/8uf7_42185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uf7_42185/04_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_42185/04_2025/8uf7_42185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uf7_42185/04_2025/8uf7_42185.map" model { file = "/net/cci-nas-00/data/ceres_data/8uf7_42185/04_2025/8uf7_42185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uf7_42185/04_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-5669/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: 3.29, per 1000 atoms: 0.84 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: 0.94 Conformation dependent library (CDL) restraints added in 486.2 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: 0.45 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: 1.01 Time building geometry restraints manager: 1.14 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: 2.060 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- 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 : 0.428 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.1272 time to fit residues: 13.7756 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 : 0.386 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163157 restraints weight = 5430.552| |-----------------------------------------------------------------------------| 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 52.668 562 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 8.22379 ( 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 : 0.460 Fit side-chains REVERT: A 38 GLN cc_start: 0.7667 (pt0) cc_final: 0.7283 (pt0) REVERT: B 232 SER cc_start: 0.4887 (OUTLIER) cc_final: 0.4404 (m) outliers start: 27 outliers final: 18 residues processed: 94 average time/residue: 0.1107 time to fit residues: 14.2070 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 : 0.451 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.178235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161047 restraints weight = 5524.983| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.03 r_work: 0.3990 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 4030 Z= 0.204 Angle : 0.690 6.615 5495 Z= 0.349 Chirality : 0.045 0.136 613 Planarity : 0.005 0.056 701 Dihedral : 5.855 55.624 562 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.80 % Favored : 86.61 % Rotamer: Outliers : 8.72 % Allowed : 35.12 % Favored : 56.15 % 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: -2.13 (0.37), residues: 508 helix: 0.04 (1.17), residues: 22 sheet: -1.31 (0.41), residues: 159 loop : -1.62 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.008 0.001 PHE A 63 TYR 0.014 0.002 TYR B 248 ARG 0.006 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 77) hydrogen bonds : angle 7.68145 ( 183) SS BOND : bond 0.00269 ( 7) SS BOND : angle 0.91070 ( 14) covalent geometry : bond 0.00473 ( 4023) covalent geometry : angle 0.68917 ( 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 121 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.384 Fit side-chains REVERT: A 38 GLN cc_start: 0.7864 (pt0) cc_final: 0.7381 (pt0) REVERT: B 232 SER cc_start: 0.4994 (OUTLIER) cc_final: 0.4535 (m) outliers start: 39 outliers final: 29 residues processed: 107 average time/residue: 0.1065 time to fit residues: 15.3550 Evaluate side-chains 110 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 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 109 LEU Chi-restraints excluded: chain C residue 139 SER 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: 0.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.177778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160419 restraints weight = 5489.418| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.03 r_work: 0.3984 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.1384 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= 0.213 Angle : 0.705 7.453 5495 Z= 0.354 Chirality : 0.045 0.148 613 Planarity : 0.005 0.057 701 Dihedral : 6.020 59.829 562 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.80 % Favored : 86.61 % Rotamer: Outliers : 9.62 % Allowed : 34.00 % Favored : 56.38 % 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: -0.25 (1.12), residues: 22 sheet: -1.28 (0.42), residues: 159 loop : -1.70 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 375 HIS 0.005 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.013 0.002 TYR B 248 ARG 0.003 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 77) hydrogen bonds : angle 7.36421 ( 183) SS BOND : bond 0.00275 ( 7) SS BOND : angle 0.88083 ( 14) covalent geometry : bond 0.00496 ( 4023) covalent geometry : angle 0.70466 ( 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 126 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.424 Fit side-chains REVERT: A 26 SER cc_start: 0.4827 (OUTLIER) cc_final: 0.3560 (p) REVERT: A 38 GLN cc_start: 0.7978 (pt0) cc_final: 0.7677 (pt0) REVERT: A 48 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.6082 (m100) REVERT: B 232 SER cc_start: 0.5012 (OUTLIER) cc_final: 0.4344 (m) outliers start: 43 outliers final: 34 residues processed: 112 average time/residue: 0.1099 time to fit residues: 16.5619 Evaluate side-chains 119 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 34 LEU 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 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 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 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 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 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 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 = 0.4295 r_free = 0.4295 target = 0.177649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159959 restraints weight = 5594.059| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.11 r_work: 0.3977 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 4030 Z= 0.204 Angle : 0.693 6.789 5495 Z= 0.350 Chirality : 0.045 0.132 613 Planarity : 0.005 0.058 701 Dihedral : 5.937 56.625 562 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.19 % Favored : 86.22 % Rotamer: Outliers : 9.62 % Allowed : 33.78 % 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: -2.27 (0.37), residues: 508 helix: -0.46 (1.12), residues: 22 sheet: -1.31 (0.42), residues: 159 loop : -1.74 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.013 0.002 TYR B 248 ARG 0.003 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 77) hydrogen bonds : angle 7.12715 ( 183) SS BOND : bond 0.00276 ( 7) SS BOND : angle 0.78700 ( 14) covalent geometry : bond 0.00474 ( 4023) covalent geometry : angle 0.69321 ( 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 126 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.436 Fit side-chains REVERT: A 26 SER cc_start: 0.4756 (OUTLIER) cc_final: 0.3611 (p) REVERT: A 38 GLN cc_start: 0.7950 (pt0) cc_final: 0.7621 (pt0) REVERT: A 48 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.6057 (m100) REVERT: B 232 SER cc_start: 0.5024 (OUTLIER) cc_final: 0.4360 (m) REVERT: B 274 TYR cc_start: 0.4739 (m-10) cc_final: 0.4483 (m-10) REVERT: B 392 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6758 (pt0) outliers start: 43 outliers final: 34 residues processed: 114 average time/residue: 0.1094 time to fit residues: 16.9120 Evaluate side-chains 119 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 34 LEU 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 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 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 337 THR Chi-restraints excluded: chain B residue 358 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 87 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.180636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.161834 restraints weight = 5454.546| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.29 r_work: 0.3949 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 4030 Z= 0.245 Angle : 0.730 7.001 5495 Z= 0.369 Chirality : 0.046 0.139 613 Planarity : 0.005 0.059 701 Dihedral : 6.073 53.581 562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.60 % Favored : 86.81 % Rotamer: Outliers : 10.29 % Allowed : 33.33 % Favored : 56.38 % 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: -2.41 (0.37), residues: 508 helix: 0.39 (1.29), residues: 16 sheet: -1.40 (0.41), residues: 159 loop : -1.88 (0.34), residues: 333 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 0.010 0.002 PHE A 63 TYR 0.013 0.002 TYR B 248 ARG 0.003 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 77) hydrogen bonds : angle 7.25264 ( 183) SS BOND : bond 0.00328 ( 7) SS BOND : angle 0.82300 ( 14) covalent geometry : bond 0.00562 ( 4023) covalent geometry : angle 0.72971 ( 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 127 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.397 Fit side-chains REVERT: A 26 SER cc_start: 0.4769 (OUTLIER) cc_final: 0.3537 (p) REVERT: A 38 GLN cc_start: 0.8021 (pt0) cc_final: 0.7576 (pt0) REVERT: A 48 TRP cc_start: 0.6523 (OUTLIER) cc_final: 0.5946 (m100) REVERT: B 232 SER cc_start: 0.4976 (OUTLIER) cc_final: 0.4324 (m) REVERT: B 392 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6835 (pt0) REVERT: C 140 ILE cc_start: 0.4611 (OUTLIER) cc_final: 0.4136 (tp) outliers start: 46 outliers final: 30 residues processed: 115 average time/residue: 0.1056 time to fit residues: 16.8617 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 : 0.400 ------------------------------------------------------------------------------- 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 34 LEU 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 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 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 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 392 GLN Chi-restraints excluded: chain B residue 409 TRP 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 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 140 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: 0.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 46 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.178545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.161120 restraints weight = 5438.736| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.04 r_work: 0.3992 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4030 Z= 0.172 Angle : 0.690 7.048 5495 Z= 0.348 Chirality : 0.046 0.253 613 Planarity : 0.005 0.060 701 Dihedral : 5.784 51.048 562 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.81 % Favored : 87.60 % Rotamer: Outliers : 8.95 % Allowed : 34.68 % Favored : 56.38 % 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: -2.38 (0.36), residues: 508 helix: 0.46 (1.28), residues: 16 sheet: -1.41 (0.41), residues: 160 loop : -1.84 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.011 0.001 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 77) hydrogen bonds : angle 6.97791 ( 183) SS BOND : bond 0.00255 ( 7) SS BOND : angle 0.94731 ( 14) covalent geometry : bond 0.00403 ( 4023) covalent geometry : angle 0.68942 ( 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 : 0.428 Fit side-chains REVERT: A 22 THR cc_start: 0.7340 (m) cc_final: 0.7078 (m) REVERT: A 26 SER cc_start: 0.4804 (OUTLIER) cc_final: 0.3620 (p) REVERT: A 38 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: A 48 TRP cc_start: 0.6481 (OUTLIER) cc_final: 0.5944 (m100) REVERT: B 232 SER cc_start: 0.5036 (OUTLIER) cc_final: 0.4377 (m) REVERT: C 140 ILE cc_start: 0.4456 (OUTLIER) cc_final: 0.3978 (tp) outliers start: 40 outliers final: 30 residues processed: 110 average time/residue: 0.1304 time to fit residues: 19.4994 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 : 0.439 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain A residue 38 GLN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.178503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161123 restraints weight = 5469.225| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.06 r_work: 0.3986 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.1838 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= 0.179 Angle : 0.694 7.212 5495 Z= 0.349 Chirality : 0.046 0.223 613 Planarity : 0.005 0.060 701 Dihedral : 5.743 48.888 562 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.01 % Favored : 87.40 % Rotamer: Outliers : 8.72 % Allowed : 34.00 % 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: -2.38 (0.36), residues: 508 helix: 0.48 (1.28), residues: 16 sheet: -1.35 (0.41), residues: 159 loop : -1.88 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.011 0.002 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 77) hydrogen bonds : angle 6.89982 ( 183) SS BOND : bond 0.00254 ( 7) SS BOND : angle 0.94348 ( 14) covalent geometry : bond 0.00420 ( 4023) covalent geometry : angle 0.69364 ( 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 121 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 1.648 Fit side-chains REVERT: A 22 THR cc_start: 0.7256 (m) cc_final: 0.6998 (m) REVERT: A 26 SER cc_start: 0.4687 (OUTLIER) cc_final: 0.3549 (p) REVERT: A 38 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: A 48 TRP cc_start: 0.6482 (OUTLIER) cc_final: 0.5952 (m100) REVERT: B 232 SER cc_start: 0.5047 (OUTLIER) cc_final: 0.4414 (m) REVERT: C 140 ILE cc_start: 0.4518 (OUTLIER) cc_final: 0.4033 (tp) outliers start: 39 outliers final: 29 residues processed: 109 average time/residue: 0.1801 time to fit residues: 28.4458 Evaluate side-chains 116 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 38 GLN 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 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 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 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: 0.9980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.178670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.161906 restraints weight = 5467.599| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.04 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: 0.6473 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 4030 Z= 0.162 Angle : 0.678 7.209 5495 Z= 0.340 Chirality : 0.045 0.187 613 Planarity : 0.005 0.060 701 Dihedral : 5.012 17.595 560 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.01 % Favored : 87.40 % Rotamer: Outliers : 8.28 % Allowed : 34.90 % 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: -2.34 (0.36), residues: 508 helix: 0.52 (1.28), residues: 16 sheet: -1.29 (0.42), residues: 159 loop : -1.88 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.010 0.001 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 77) hydrogen bonds : angle 6.77965 ( 183) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.82747 ( 14) covalent geometry : bond 0.00381 ( 4023) covalent geometry : angle 0.67807 ( 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 116 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.592 Fit side-chains REVERT: A 22 THR cc_start: 0.7166 (m) cc_final: 0.6917 (m) REVERT: A 26 SER cc_start: 0.4615 (OUTLIER) cc_final: 0.3460 (p) REVERT: A 38 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: A 48 TRP cc_start: 0.6429 (OUTLIER) cc_final: 0.5909 (m100) REVERT: B 232 SER cc_start: 0.5062 (OUTLIER) cc_final: 0.4431 (m) REVERT: C 140 ILE cc_start: 0.4314 (OUTLIER) cc_final: 0.3843 (tp) outliers start: 37 outliers final: 29 residues processed: 105 average time/residue: 0.1671 time to fit residues: 23.5485 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 : 0.394 ------------------------------------------------------------------------------- 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 38 GLN 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 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 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 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 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: 0.9990 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.181745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163115 restraints weight = 5530.456| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.38 r_work: 0.3987 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 4030 Z= 0.179 Angle : 0.695 7.803 5495 Z= 0.348 Chirality : 0.046 0.198 613 Planarity : 0.005 0.059 701 Dihedral : 5.102 18.626 560 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.20 % Favored : 87.20 % Rotamer: Outliers : 8.05 % Allowed : 35.79 % Favored : 56.15 % 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 (0.36), residues: 508 helix: 0.39 (1.27), residues: 16 sheet: -1.02 (0.43), residues: 147 loop : -2.01 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.011 0.001 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 77) hydrogen bonds : angle 6.81127 ( 183) SS BOND : bond 0.00251 ( 7) SS BOND : angle 0.82869 ( 14) covalent geometry : bond 0.00421 ( 4023) covalent geometry : angle 0.69472 ( 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 115 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.393 Fit side-chains REVERT: A 21 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5405 (ttm) REVERT: A 22 THR cc_start: 0.7190 (m) cc_final: 0.6964 (m) REVERT: A 26 SER cc_start: 0.4691 (OUTLIER) cc_final: 0.3548 (p) REVERT: A 38 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: A 48 TRP cc_start: 0.6494 (OUTLIER) cc_final: 0.5955 (m100) REVERT: B 232 SER cc_start: 0.5047 (OUTLIER) cc_final: 0.4407 (m) REVERT: C 140 ILE cc_start: 0.4476 (OUTLIER) cc_final: 0.3972 (tp) outliers start: 36 outliers final: 30 residues processed: 103 average time/residue: 0.1012 time to fit residues: 14.4706 Evaluate side-chains 115 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 38 GLN 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 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 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 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: 0.8980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.180963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.162486 restraints weight = 5392.460| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.35 r_work: 0.3980 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 4030 Z= 0.201 Angle : 0.709 7.203 5495 Z= 0.356 Chirality : 0.046 0.207 613 Planarity : 0.005 0.060 701 Dihedral : 5.207 19.471 560 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.60 % Favored : 86.81 % Rotamer: Outliers : 8.72 % Allowed : 34.90 % Favored : 56.38 % 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: -2.40 (0.36), residues: 508 helix: 0.31 (1.28), residues: 16 sheet: -1.08 (0.43), residues: 147 loop : -2.04 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.010 0.002 PHE A 140 TYR 0.011 0.002 TYR B 248 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 77) hydrogen bonds : angle 6.86917 ( 183) SS BOND : bond 0.00259 ( 7) SS BOND : angle 0.80684 ( 14) covalent geometry : bond 0.00466 ( 4023) covalent geometry : angle 0.70881 ( 5481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.02 seconds wall clock time: 42 minutes 21.02 seconds (2541.02 seconds total)