Starting phenix.real_space_refine on Wed Jun 3 22:29:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h8n_51937/06_2026/9h8n_51937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h8n_51937/06_2026/9h8n_51937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h8n_51937/06_2026/9h8n_51937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h8n_51937/06_2026/9h8n_51937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h8n_51937/06_2026/9h8n_51937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h8n_51937/06_2026/9h8n_51937.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5612 2.51 5 N 1456 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4371 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 17, 'TRANS': 550} Restraints were copied for chains: B Time building chain proxies: 3.25, per 1000 atoms: 0.37 Number of scatterers: 8742 At special positions: 0 Unit cell: (114.49, 78.11, 134.82, 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 36 16.00 O 1638 8.00 N 1456 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 270.0 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 64.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.646A pdb=" N PHE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 64 through 109 removed outlier: 3.516A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 4.158A pdb=" N THR A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 117' Processing helix chain 'A' and resid 120 through 140 removed outlier: 4.278A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 274 removed outlier: 3.738A pdb=" N ARG A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.694A pdb=" N PHE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 322 removed outlier: 3.756A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 321 " --> pdb=" O MET A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 481 through 495 removed outlier: 4.263A pdb=" N ILE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.645A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 64 through 109 removed outlier: 3.516A pdb=" N LYS B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 4.159A pdb=" N THR B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 117' Processing helix chain 'B' and resid 120 through 140 removed outlier: 4.278A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 164 through 210 Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 274 removed outlier: 3.739A pdb=" N ARG B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.695A pdb=" N PHE B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 322 removed outlier: 3.757A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 321 " --> pdb=" O MET B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 446 through 455 Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 481 through 495 removed outlier: 4.264A pdb=" N ILE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 488 " --> pdb=" O ARG B 484 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 571 through 575 500 hydrogen bonds defined for protein. 1494 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: 1.25 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2289 1.33 - 1.46: 1431 1.46 - 1.58: 5088 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 8876 Sorted by residual: bond pdb=" CA ASN B 496 " pdb=" C ASN B 496 " ideal model delta sigma weight residual 1.532 1.558 -0.026 6.50e-03 2.37e+04 1.63e+01 bond pdb=" CA ASN A 496 " pdb=" C ASN A 496 " ideal model delta sigma weight residual 1.532 1.558 -0.026 6.50e-03 2.37e+04 1.58e+01 bond pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.28e-02 6.10e+03 8.90e+00 bond pdb=" N ARG B 228 " pdb=" CA ARG B 228 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.28e-02 6.10e+03 8.72e+00 bond pdb=" CA ILE B 108 " pdb=" C ILE B 108 " ideal model delta sigma weight residual 1.520 1.553 -0.034 1.26e-02 6.30e+03 7.07e+00 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 9814 1.41 - 2.82: 1577 2.82 - 4.23: 508 4.23 - 5.63: 99 5.63 - 7.04: 14 Bond angle restraints: 12012 Sorted by residual: angle pdb=" CB HIS A 535 " pdb=" CG HIS A 535 " pdb=" CD2 HIS A 535 " ideal model delta sigma weight residual 131.20 124.37 6.83 1.30e+00 5.92e-01 2.76e+01 angle pdb=" CB HIS B 535 " pdb=" CG HIS B 535 " pdb=" CD2 HIS B 535 " ideal model delta sigma weight residual 131.20 124.37 6.83 1.30e+00 5.92e-01 2.76e+01 angle pdb=" C ILE A 213 " pdb=" N ARG A 214 " pdb=" CA ARG A 214 " ideal model delta sigma weight residual 120.28 126.90 -6.62 1.34e+00 5.57e-01 2.44e+01 angle pdb=" C ILE B 213 " pdb=" N ARG B 214 " pdb=" CA ARG B 214 " ideal model delta sigma weight residual 120.28 126.90 -6.62 1.34e+00 5.57e-01 2.44e+01 angle pdb=" OE1 GLN A 208 " pdb=" CD GLN A 208 " pdb=" NE2 GLN A 208 " ideal model delta sigma weight residual 122.60 117.78 4.82 1.00e+00 1.00e+00 2.32e+01 ... (remaining 12007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 4796 15.66 - 31.31: 436 31.31 - 46.97: 108 46.97 - 62.63: 12 62.63 - 78.29: 18 Dihedral angle restraints: 5370 sinusoidal: 2118 harmonic: 3252 Sorted by residual: dihedral pdb=" CA CYS A 428 " pdb=" C CYS A 428 " pdb=" N GLY A 429 " pdb=" CA GLY A 429 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA CYS B 428 " pdb=" C CYS B 428 " pdb=" N GLY B 429 " pdb=" CA GLY B 429 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER A 436 " pdb=" C SER A 436 " pdb=" N TYR A 437 " pdb=" CA TYR A 437 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1070 0.061 - 0.122: 284 0.122 - 0.183: 84 0.183 - 0.245: 10 0.245 - 0.306: 4 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA MET B 427 " pdb=" N MET B 427 " pdb=" C MET B 427 " pdb=" CB MET B 427 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA MET A 427 " pdb=" N MET A 427 " pdb=" C MET A 427 " pdb=" CB MET A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ARG B 491 " pdb=" N ARG B 491 " pdb=" C ARG B 491 " pdb=" CB ARG B 491 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1449 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 535 " -0.051 2.00e-02 2.50e+03 3.79e-02 2.15e+01 pdb=" CG HIS A 535 " 0.057 2.00e-02 2.50e+03 pdb=" ND1 HIS A 535 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 535 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS A 535 " -0.027 2.00e-02 2.50e+03 pdb=" NE2 HIS A 535 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 535 " 0.050 2.00e-02 2.50e+03 3.77e-02 2.13e+01 pdb=" CG HIS B 535 " -0.057 2.00e-02 2.50e+03 pdb=" ND1 HIS B 535 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS B 535 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 535 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 HIS B 535 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 226 " -0.059 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR B 226 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 226 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 226 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 226 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 226 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 226 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 226 " -0.035 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 518 2.74 - 3.28: 9365 3.28 - 3.82: 13591 3.82 - 4.36: 16425 4.36 - 4.90: 27482 Nonbonded interactions: 67381 Sorted by model distance: nonbonded pdb=" NZ LYS A 230 " pdb=" OE2 GLU B 101 " model vdw 2.202 3.120 nonbonded pdb=" OG SER A 511 " pdb=" OE1 GLU A 514 " model vdw 2.209 3.040 nonbonded pdb=" OG SER B 511 " pdb=" OE1 GLU B 514 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU A 101 " pdb=" NZ LYS B 230 " model vdw 2.252 3.120 nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 437 " model vdw 2.273 3.040 ... (remaining 67376 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.380 Find NCS groups from input model: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.038 8876 Z= 0.539 Angle : 1.212 7.044 12012 Z= 0.793 Chirality : 0.061 0.306 1452 Planarity : 0.007 0.064 1508 Dihedral : 13.730 78.285 3282 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1132 helix: 1.11 (0.19), residues: 706 sheet: 1.75 (0.77), residues: 44 loop : -1.37 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 201 TYR 0.059 0.008 TYR B 226 PHE 0.046 0.005 PHE B 348 TRP 0.047 0.014 TRP B 164 HIS 0.009 0.002 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.54 ( 8876) covalent geometry : angle 1.21237 / 0.79 (12012) hydrogen bonds : bond 0.12944 / 8.68 ( 500) hydrogen bonds : angle 5.43205 / 3.98 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.351 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0964 time to fit residues: 17.1283 Evaluate side-chains 80 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 485 GLN B 208 GLN B 485 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088070 restraints weight = 18497.978| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.24 r_work: 0.3305 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8876 Z= 0.188 Angle : 0.651 6.403 12012 Z= 0.332 Chirality : 0.043 0.161 1452 Planarity : 0.004 0.039 1508 Dihedral : 4.407 16.855 1216 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.71 % Allowed : 10.44 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1132 helix: 1.72 (0.20), residues: 712 sheet: 1.90 (0.72), residues: 48 loop : -0.77 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 557 TYR 0.014 0.001 TYR A 289 PHE 0.014 0.002 PHE A 160 TRP 0.018 0.002 TRP A 164 HIS 0.004 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 8876) covalent geometry : angle 0.65063 / 0.33 (12012) hydrogen bonds : bond 0.04635 / 3.11 ( 500) hydrogen bonds : angle 4.19212 / 3.06 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6135 (ptp) REVERT: A 188 MET cc_start: 0.8457 (mmm) cc_final: 0.8244 (mmm) REVERT: A 193 ARG cc_start: 0.8178 (mmp80) cc_final: 0.7866 (mmp80) REVERT: A 196 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 286 PHE cc_start: 0.8303 (t80) cc_final: 0.8045 (t80) REVERT: A 454 MET cc_start: 0.8896 (mmm) cc_final: 0.8451 (mpp) REVERT: A 500 LEU cc_start: 0.8907 (tp) cc_final: 0.8506 (mp) REVERT: A 570 TYR cc_start: 0.7850 (t80) cc_final: 0.7647 (t80) REVERT: B 286 PHE cc_start: 0.8332 (t80) cc_final: 0.8072 (t80) REVERT: B 454 MET cc_start: 0.8531 (mtm) cc_final: 0.8162 (mtm) REVERT: B 500 LEU cc_start: 0.8910 (tp) cc_final: 0.8511 (mp) outliers start: 26 outliers final: 13 residues processed: 97 average time/residue: 0.0890 time to fit residues: 12.4391 Evaluate side-chains 81 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.0970 chunk 53 optimal weight: 0.0050 chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 104 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 72 optimal weight: 0.0030 overall best weight: 0.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 560 HIS B 485 GLN B 560 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.121894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.091993 restraints weight = 18078.297| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.85 r_work: 0.3353 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8876 Z= 0.113 Angle : 0.532 7.749 12012 Z= 0.275 Chirality : 0.038 0.143 1452 Planarity : 0.003 0.026 1508 Dihedral : 4.094 21.600 1216 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.88 % Allowed : 11.90 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.25), residues: 1132 helix: 2.05 (0.20), residues: 706 sheet: 0.97 (0.61), residues: 70 loop : -0.57 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.016 0.001 TYR B 570 PHE 0.010 0.001 PHE A 160 TRP 0.008 0.001 TRP A 164 HIS 0.008 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 8876) covalent geometry : angle 0.53187 / 0.28 (12012) hydrogen bonds : bond 0.04022 / 2.70 ( 500) hydrogen bonds : angle 3.87762 / 2.84 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8155 (tt) REVERT: A 286 PHE cc_start: 0.8262 (t80) cc_final: 0.7972 (t80) REVERT: A 454 MET cc_start: 0.8900 (mmm) cc_final: 0.8430 (mpp) REVERT: A 564 MET cc_start: 0.8489 (mtm) cc_final: 0.8186 (mtm) REVERT: B 96 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8130 (tt) REVERT: B 188 MET cc_start: 0.8438 (mmm) cc_final: 0.8228 (mmm) REVERT: B 286 PHE cc_start: 0.8214 (t80) cc_final: 0.7983 (t80) REVERT: B 564 MET cc_start: 0.8493 (mtm) cc_final: 0.8223 (mtm) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 0.0918 time to fit residues: 11.3182 Evaluate side-chains 70 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.0030 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.119702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088208 restraints weight = 18600.892| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.21 r_work: 0.3306 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8876 Z= 0.117 Angle : 0.515 8.514 12012 Z= 0.263 Chirality : 0.038 0.136 1452 Planarity : 0.003 0.028 1508 Dihedral : 3.927 21.470 1216 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.67 % Allowed : 13.26 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.25), residues: 1132 helix: 2.12 (0.20), residues: 706 sheet: 1.13 (0.61), residues: 70 loop : -0.54 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 571 TYR 0.014 0.001 TYR A 570 PHE 0.009 0.001 PHE B 390 TRP 0.009 0.001 TRP B 164 HIS 0.002 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8876) covalent geometry : angle 0.51464 / 0.26 (12012) hydrogen bonds : bond 0.03875 / 2.59 ( 500) hydrogen bonds : angle 3.76420 / 2.74 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6194 (ptt) cc_final: 0.4786 (ppp) REVERT: A 286 PHE cc_start: 0.8364 (t80) cc_final: 0.8079 (t80) REVERT: A 454 MET cc_start: 0.8896 (mmm) cc_final: 0.8460 (mpp) REVERT: B 188 MET cc_start: 0.8466 (mmm) cc_final: 0.8218 (mmm) REVERT: B 286 PHE cc_start: 0.8327 (t80) cc_final: 0.8089 (t80) REVERT: B 454 MET cc_start: 0.8569 (mtm) cc_final: 0.8121 (mtm) REVERT: B 564 MET cc_start: 0.8533 (mtm) cc_final: 0.8209 (mtm) outliers start: 16 outliers final: 10 residues processed: 75 average time/residue: 0.0780 time to fit residues: 8.7907 Evaluate side-chains 69 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS B 416 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.119653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.087811 restraints weight = 18535.165| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.23 r_work: 0.3299 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8876 Z= 0.105 Angle : 0.490 9.163 12012 Z= 0.251 Chirality : 0.037 0.131 1452 Planarity : 0.003 0.026 1508 Dihedral : 3.748 19.360 1216 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.25 % Allowed : 13.67 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1132 helix: 2.24 (0.20), residues: 706 sheet: 1.17 (0.62), residues: 70 loop : -0.50 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 571 TYR 0.025 0.001 TYR A 570 PHE 0.009 0.001 PHE A 390 TRP 0.009 0.001 TRP B 164 HIS 0.002 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 8876) covalent geometry : angle 0.48973 / 0.25 (12012) hydrogen bonds : bond 0.03677 / 2.45 ( 500) hydrogen bonds : angle 3.63584 / 2.63 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6205 (ptt) cc_final: 0.4896 (ppp) REVERT: A 286 PHE cc_start: 0.8349 (t80) cc_final: 0.8107 (t80) REVERT: B 188 MET cc_start: 0.8493 (mmm) cc_final: 0.8241 (mmm) REVERT: B 286 PHE cc_start: 0.8318 (t80) cc_final: 0.8115 (t80) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.0888 time to fit residues: 9.6004 Evaluate side-chains 67 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.119189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088680 restraints weight = 18577.394| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.95 r_work: 0.3292 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8876 Z= 0.110 Angle : 0.503 9.844 12012 Z= 0.254 Chirality : 0.037 0.133 1452 Planarity : 0.003 0.026 1508 Dihedral : 3.691 18.018 1216 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.15 % Allowed : 15.45 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1132 helix: 2.29 (0.20), residues: 708 sheet: 1.04 (0.60), residues: 74 loop : -0.53 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.024 0.001 TYR B 570 PHE 0.011 0.001 PHE A 460 TRP 0.010 0.001 TRP A 104 HIS 0.002 0.000 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 8876) covalent geometry : angle 0.50278 / 0.25 (12012) hydrogen bonds : bond 0.03630 / 2.42 ( 500) hydrogen bonds : angle 3.57853 / 2.59 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.8354 (t80) cc_final: 0.8116 (t80) REVERT: A 354 GLN cc_start: 0.5774 (tm-30) cc_final: 0.5515 (tm-30) REVERT: A 454 MET cc_start: 0.8947 (mmm) cc_final: 0.8427 (mpp) REVERT: B 188 MET cc_start: 0.8496 (mmm) cc_final: 0.8246 (mmm) REVERT: B 454 MET cc_start: 0.8562 (mtm) cc_final: 0.7835 (mtm) REVERT: B 564 MET cc_start: 0.8483 (mtm) cc_final: 0.8227 (mtm) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.0795 time to fit residues: 8.7899 Evaluate side-chains 67 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** 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 = 0.3952 r_free = 0.3952 target = 0.118514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089811 restraints weight = 18610.050| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.60 r_work: 0.3308 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8876 Z= 0.115 Angle : 0.520 10.466 12012 Z= 0.258 Chirality : 0.038 0.203 1452 Planarity : 0.003 0.027 1508 Dihedral : 3.696 18.327 1216 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.57 % Allowed : 15.34 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1132 helix: 2.26 (0.20), residues: 718 sheet: 1.10 (0.60), residues: 74 loop : -0.72 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 571 TYR 0.009 0.001 TYR A 570 PHE 0.009 0.001 PHE A 57 TRP 0.006 0.001 TRP A 164 HIS 0.002 0.000 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8876) covalent geometry : angle 0.52016 / 0.26 (12012) hydrogen bonds : bond 0.03621 / 2.42 ( 500) hydrogen bonds : angle 3.56710 / 2.57 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.8967 (mmm) cc_final: 0.8430 (mpp) REVERT: B 188 MET cc_start: 0.8506 (mmm) cc_final: 0.8294 (mmm) REVERT: B 344 ASP cc_start: 0.7905 (t0) cc_final: 0.6787 (p0) REVERT: B 454 MET cc_start: 0.8502 (mtm) cc_final: 0.7784 (mtm) outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 0.0877 time to fit residues: 9.5750 Evaluate side-chains 65 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.0030 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.5350 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.118228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087373 restraints weight = 18523.985| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.97 r_work: 0.3274 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8876 Z= 0.111 Angle : 0.522 9.534 12012 Z= 0.257 Chirality : 0.037 0.134 1452 Planarity : 0.003 0.027 1508 Dihedral : 3.676 18.188 1216 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.15 % Allowed : 16.60 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.25), residues: 1132 helix: 2.29 (0.20), residues: 720 sheet: 1.27 (0.62), residues: 74 loop : -0.65 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 571 TYR 0.036 0.001 TYR A 570 PHE 0.009 0.001 PHE A 460 TRP 0.006 0.001 TRP B 164 HIS 0.002 0.000 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 8876) covalent geometry : angle 0.52190 / 0.26 (12012) hydrogen bonds : bond 0.03571 / 2.38 ( 500) hydrogen bonds : angle 3.54024 / 2.56 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.8952 (mmm) cc_final: 0.8416 (mpp) REVERT: B 392 SER cc_start: 0.8677 (t) cc_final: 0.8475 (t) REVERT: B 454 MET cc_start: 0.8559 (mtm) cc_final: 0.7773 (mtm) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.0734 time to fit residues: 7.9650 Evaluate side-chains 67 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.117714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088452 restraints weight = 18573.435| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.08 r_work: 0.3261 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8876 Z= 0.119 Angle : 0.532 11.786 12012 Z= 0.262 Chirality : 0.037 0.132 1452 Planarity : 0.003 0.027 1508 Dihedral : 3.651 17.125 1216 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.04 % Allowed : 17.01 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1132 helix: 2.27 (0.20), residues: 720 sheet: 1.28 (0.62), residues: 74 loop : -0.65 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 193 TYR 0.009 0.001 TYR A 570 PHE 0.015 0.001 PHE A 57 TRP 0.006 0.001 TRP A 164 HIS 0.002 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8876) covalent geometry : angle 0.53209 / 0.26 (12012) hydrogen bonds : bond 0.03639 / 2.43 ( 500) hydrogen bonds : angle 3.55322 / 2.57 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.8953 (mmm) cc_final: 0.8421 (mpp) REVERT: B 454 MET cc_start: 0.8556 (mtm) cc_final: 0.7792 (mtm) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0824 time to fit residues: 8.4872 Evaluate side-chains 64 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.117448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088164 restraints weight = 18497.131| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.08 r_work: 0.3254 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8876 Z= 0.121 Angle : 0.549 11.802 12012 Z= 0.270 Chirality : 0.039 0.310 1452 Planarity : 0.003 0.027 1508 Dihedral : 3.684 16.444 1216 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.73 % Allowed : 17.43 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1132 helix: 2.15 (0.20), residues: 732 sheet: 1.27 (0.61), residues: 74 loop : -0.68 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 536 TYR 0.041 0.001 TYR B 570 PHE 0.016 0.001 PHE A 57 TRP 0.006 0.001 TRP B 164 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8876) covalent geometry : angle 0.54921 / 0.27 (12012) hydrogen bonds : bond 0.03666 / 2.45 ( 500) hydrogen bonds : angle 3.57989 / 2.60 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.8955 (mmm) cc_final: 0.8422 (mpp) REVERT: B 454 MET cc_start: 0.8545 (mtm) cc_final: 0.7801 (mtm) outliers start: 7 outliers final: 7 residues processed: 62 average time/residue: 0.0797 time to fit residues: 7.7098 Evaluate side-chains 64 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.3980 chunk 40 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 54 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.086831 restraints weight = 18959.955| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.85 r_work: 0.3327 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8876 Z= 0.105 Angle : 0.544 11.318 12012 Z= 0.268 Chirality : 0.038 0.240 1452 Planarity : 0.003 0.027 1508 Dihedral : 3.663 15.757 1216 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.04 % Allowed : 17.54 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.26), residues: 1132 helix: 2.22 (0.20), residues: 732 sheet: 1.28 (0.62), residues: 74 loop : -0.66 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 193 TYR 0.053 0.001 TYR A 570 PHE 0.009 0.001 PHE A 460 TRP 0.005 0.001 TRP B 164 HIS 0.002 0.000 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 8876) covalent geometry : angle 0.54381 / 0.27 (12012) hydrogen bonds : bond 0.03493 / 2.34 ( 500) hydrogen bonds : angle 3.50667 / 2.55 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.09 seconds wall clock time: 36 minutes 3.94 seconds (2163.94 seconds total)