Starting phenix.real_space_refine on Fri Aug 22 13:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6b_41068/08_2025/8t6b_41068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6b_41068/08_2025/8t6b_41068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6b_41068/08_2025/8t6b_41068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6b_41068/08_2025/8t6b_41068.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6b_41068/08_2025/8t6b_41068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6b_41068/08_2025/8t6b_41068.cif" } resolution = 3.72 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= 0.001 sd= 0.017 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 28 5.16 5 C 1940 2.51 5 N 455 2.21 5 O 493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2916 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2903 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 23, 'TRANS': 363} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.74, per 1000 atoms: 0.25 Number of scatterers: 2916 At special positions: 0 Unit cell: (76.582, 66.198, 72.688, 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 28 16.00 O 493 8.00 N 455 7.00 C 1940 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: 0.15 Conformation dependent library (CDL) restraints added in 108.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.619A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.696A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix removed outlier: 3.508A pdb=" N LYS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.388A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.560A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 212 removed outlier: 4.014A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 5.039A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.679A pdb=" N MET A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 4.094A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 4.658A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.866A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.619A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.918A pdb=" N LEU A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.638A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.679A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 412 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 447 removed outlier: 3.881A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.016A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.694A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.864A pdb=" N SER A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 606 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 873 1.35 - 1.46: 702 1.46 - 1.58: 1363 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 2986 Sorted by residual: bond pdb=" CG LEU A 409 " pdb=" CD1 LEU A 409 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" C ALA A 464 " pdb=" N PRO A 465 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.19e-02 7.06e+03 2.74e+00 bond pdb=" CA VAL A 41 " pdb=" CB VAL A 41 " ideal model delta sigma weight residual 1.534 1.544 -0.010 6.80e-03 2.16e+04 2.03e+00 bond pdb=" CA VAL A 41 " pdb=" C VAL A 41 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.58e+00 bond pdb=" CA SER A 400 " pdb=" C SER A 400 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.41e-02 5.03e+03 1.41e+00 ... (remaining 2981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3917 1.78 - 3.56: 105 3.56 - 5.33: 28 5.33 - 7.11: 6 7.11 - 8.89: 3 Bond angle restraints: 4059 Sorted by residual: angle pdb=" C GLY A 247 " pdb=" N LYS A 248 " pdb=" CA LYS A 248 " ideal model delta sigma weight residual 120.28 124.94 -4.66 1.34e+00 5.57e-01 1.21e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.41 -6.60 2.21e+00 2.05e-01 8.93e+00 angle pdb=" C VAL A 40 " pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta sigma weight residual 120.24 122.06 -1.82 6.30e-01 2.52e+00 8.34e+00 angle pdb=" C PHE A 463 " pdb=" N ALA A 464 " pdb=" CA ALA A 464 " ideal model delta sigma weight residual 120.58 124.34 -3.76 1.32e+00 5.74e-01 8.10e+00 angle pdb=" N ILE A 447 " pdb=" CA ILE A 447 " pdb=" C ILE A 447 " ideal model delta sigma weight residual 113.71 111.17 2.54 9.50e-01 1.11e+00 7.14e+00 ... (remaining 4054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1531 15.53 - 31.06: 160 31.06 - 46.59: 52 46.59 - 62.12: 6 62.12 - 77.65: 3 Dihedral angle restraints: 1752 sinusoidal: 657 harmonic: 1095 Sorted by residual: dihedral pdb=" CA PHE A 184 " pdb=" C PHE A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASN A 34 " pdb=" C ASN A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA THR A 38 " pdb=" C THR A 38 " pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 272 0.028 - 0.057: 127 0.057 - 0.085: 51 0.085 - 0.113: 30 0.113 - 0.142: 3 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA VAL A 417 " pdb=" N VAL A 417 " pdb=" C VAL A 417 " pdb=" CB VAL A 417 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO A 161 " pdb=" N PRO A 161 " pdb=" C PRO A 161 " pdb=" CB PRO A 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL A 415 " pdb=" N VAL A 415 " pdb=" C VAL A 415 " pdb=" CB VAL A 415 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 480 not shown) Planarity restraints: 497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 244 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CD GLU A 244 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 244 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 244 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 312 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 313 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.023 5.00e-02 4.00e+02 ... (remaining 494 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 576 2.77 - 3.30: 2987 3.30 - 3.83: 4767 3.83 - 4.37: 5321 4.37 - 4.90: 9352 Nonbonded interactions: 23003 Sorted by model distance: nonbonded pdb=" OH TYR A 293 " pdb=" O PHE A 469 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A 212 " pdb=" N ASP A 213 " model vdw 2.434 3.120 nonbonded pdb=" O TYR A 211 " pdb=" OG1 THR A 212 " model vdw 2.475 3.040 nonbonded pdb=" OH TYR A 158 " pdb=" OE2 GLU A 278 " model vdw 2.497 3.040 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.499 3.120 ... (remaining 22998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.700 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.004 0.058 2986 Z= 0.173 Angle : 0.785 8.888 4059 Z= 0.419 Chirality : 0.042 0.142 483 Planarity : 0.006 0.045 497 Dihedral : 14.454 77.650 1054 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.42), residues: 383 helix: -0.53 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.62 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 19 TYR 0.008 0.001 TYR A 341 PHE 0.012 0.001 PHE A 27 TRP 0.013 0.002 TRP A 358 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2986) covalent geometry : angle 0.78471 ( 4059) hydrogen bonds : bond 0.14913 ( 207) hydrogen bonds : angle 6.11329 ( 606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.074 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0392 time to fit residues: 2.5732 Evaluate side-chains 49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.209019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.185964 restraints weight = 3571.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189085 restraints weight = 2505.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191075 restraints weight = 1933.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.193028 restraints weight = 1606.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.193914 restraints weight = 1388.291| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2986 Z= 0.144 Angle : 0.684 6.788 4059 Z= 0.339 Chirality : 0.043 0.161 483 Planarity : 0.006 0.043 497 Dihedral : 6.587 59.237 409 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.53 % Allowed : 17.31 % Favored : 79.17 % 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 aren not related in a simple way. whole: -0.67 (0.43), residues: 383 helix: -0.06 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.51 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.016 0.001 TYR A 243 PHE 0.016 0.001 PHE A 468 TRP 0.010 0.002 TRP A 328 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2986) covalent geometry : angle 0.68438 ( 4059) hydrogen bonds : bond 0.04033 ( 207) hydrogen bonds : angle 4.62890 ( 606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.124 Fit side-chains REVERT: A 365 MET cc_start: 0.5652 (mmm) cc_final: 0.5332 (mmm) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.0430 time to fit residues: 3.3466 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.212299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192175 restraints weight = 3665.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.195137 restraints weight = 2567.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.196949 restraints weight = 1991.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.198486 restraints weight = 1661.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.199752 restraints weight = 1437.226| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2986 Z= 0.138 Angle : 0.672 6.876 4059 Z= 0.333 Chirality : 0.043 0.150 483 Planarity : 0.006 0.041 497 Dihedral : 5.978 43.802 409 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.81 % Allowed : 16.99 % Favored : 78.21 % 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 aren not related in a simple way. whole: -0.51 (0.43), residues: 383 helix: 0.12 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.69 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 326 TYR 0.014 0.001 TYR A 243 PHE 0.011 0.001 PHE A 27 TRP 0.007 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2986) covalent geometry : angle 0.67229 ( 4059) hydrogen bonds : bond 0.03693 ( 207) hydrogen bonds : angle 4.45415 ( 606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.101 Fit side-chains REVERT: A 148 PHE cc_start: 0.6376 (m-10) cc_final: 0.4678 (t80) REVERT: A 365 MET cc_start: 0.5790 (mmm) cc_final: 0.5292 (mmm) outliers start: 15 outliers final: 8 residues processed: 61 average time/residue: 0.0493 time to fit residues: 3.9580 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.213812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.192511 restraints weight = 3682.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195496 restraints weight = 2545.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197839 restraints weight = 1950.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.199016 restraints weight = 1598.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.200199 restraints weight = 1405.554| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2986 Z= 0.131 Angle : 0.705 14.815 4059 Z= 0.333 Chirality : 0.042 0.161 483 Planarity : 0.006 0.038 497 Dihedral : 5.560 31.340 409 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.45 % Allowed : 16.67 % Favored : 77.88 % 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 aren not related in a simple way. whole: -0.44 (0.43), residues: 383 helix: 0.19 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.76 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 326 TYR 0.008 0.001 TYR A 243 PHE 0.012 0.001 PHE A 468 TRP 0.008 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2986) covalent geometry : angle 0.70546 ( 4059) hydrogen bonds : bond 0.03408 ( 207) hydrogen bonds : angle 4.28518 ( 606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.109 Fit side-chains REVERT: A 148 PHE cc_start: 0.6394 (m-10) cc_final: 0.4851 (t80) REVERT: A 365 MET cc_start: 0.5756 (mmm) cc_final: 0.5171 (mmm) REVERT: A 389 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5191 (t80) outliers start: 17 outliers final: 11 residues processed: 58 average time/residue: 0.0495 time to fit residues: 3.7036 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 20 optimal weight: 0.0040 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.210078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184428 restraints weight = 3538.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.188275 restraints weight = 2213.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191422 restraints weight = 1568.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.193423 restraints weight = 1210.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194637 restraints weight = 999.851| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2986 Z= 0.130 Angle : 0.686 11.412 4059 Z= 0.323 Chirality : 0.042 0.159 483 Planarity : 0.006 0.037 497 Dihedral : 5.348 39.853 409 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 6.73 % Allowed : 16.03 % Favored : 77.24 % 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 aren not related in a simple way. whole: -0.35 (0.44), residues: 383 helix: 0.24 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.70 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.007 0.001 TYR A 211 PHE 0.010 0.001 PHE A 27 TRP 0.007 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2986) covalent geometry : angle 0.68589 ( 4059) hydrogen bonds : bond 0.03348 ( 207) hydrogen bonds : angle 4.24470 ( 606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.126 Fit side-chains REVERT: A 148 PHE cc_start: 0.6368 (m-10) cc_final: 0.4764 (t80) REVERT: A 365 MET cc_start: 0.5899 (mmm) cc_final: 0.5280 (mmm) REVERT: A 389 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5179 (t80) outliers start: 21 outliers final: 12 residues processed: 64 average time/residue: 0.0463 time to fit residues: 3.8990 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.203627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.181369 restraints weight = 3842.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184086 restraints weight = 2766.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.186392 restraints weight = 2174.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.187682 restraints weight = 1813.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.188915 restraints weight = 1596.641| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2986 Z= 0.151 Angle : 0.712 10.102 4059 Z= 0.340 Chirality : 0.043 0.166 483 Planarity : 0.006 0.049 497 Dihedral : 5.624 48.920 409 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.77 % Allowed : 17.95 % Favored : 76.28 % 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 aren not related in a simple way. whole: -0.49 (0.44), residues: 383 helix: 0.10 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.62 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.009 0.001 TYR A 211 PHE 0.012 0.001 PHE A 468 TRP 0.007 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2986) covalent geometry : angle 0.71215 ( 4059) hydrogen bonds : bond 0.03559 ( 207) hydrogen bonds : angle 4.31198 ( 606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.106 Fit side-chains REVERT: A 148 PHE cc_start: 0.6391 (m-10) cc_final: 0.4849 (t80) REVERT: A 169 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5046 (mtt) REVERT: A 365 MET cc_start: 0.5947 (mmm) cc_final: 0.5327 (mmm) REVERT: A 389 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5286 (t80) outliers start: 18 outliers final: 12 residues processed: 58 average time/residue: 0.0437 time to fit residues: 3.3423 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.0670 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.210376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.189648 restraints weight = 3787.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.191598 restraints weight = 3212.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.193484 restraints weight = 2703.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194360 restraints weight = 2047.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.194612 restraints weight = 1636.511| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2986 Z= 0.120 Angle : 0.693 8.660 4059 Z= 0.320 Chirality : 0.041 0.151 483 Planarity : 0.006 0.043 497 Dihedral : 5.312 46.769 409 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.17 % Allowed : 19.87 % Favored : 75.96 % 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 aren not related in a simple way. whole: -0.18 (0.44), residues: 383 helix: 0.37 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.71 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.005 0.001 TYR A 243 PHE 0.007 0.001 PHE A 27 TRP 0.007 0.001 TRP A 358 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 2986) covalent geometry : angle 0.69252 ( 4059) hydrogen bonds : bond 0.03030 ( 207) hydrogen bonds : angle 4.18605 ( 606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.116 Fit side-chains REVERT: A 148 PHE cc_start: 0.6272 (m-10) cc_final: 0.4923 (t80) REVERT: A 169 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.4910 (mtt) REVERT: A 359 LEU cc_start: 0.6801 (mt) cc_final: 0.6408 (mp) REVERT: A 365 MET cc_start: 0.5794 (mmm) cc_final: 0.5184 (mmm) REVERT: A 389 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5237 (t80) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.0569 time to fit residues: 4.2137 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.208544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.186525 restraints weight = 3795.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.189612 restraints weight = 2672.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191856 restraints weight = 2061.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.192974 restraints weight = 1706.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.194172 restraints weight = 1511.227| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2986 Z= 0.123 Angle : 0.702 7.954 4059 Z= 0.322 Chirality : 0.042 0.158 483 Planarity : 0.006 0.039 497 Dihedral : 5.273 47.408 409 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.81 % Allowed : 19.55 % Favored : 75.64 % 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 aren not related in a simple way. whole: -0.06 (0.44), residues: 383 helix: 0.40 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -1.48 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.007 0.001 TYR A 211 PHE 0.009 0.001 PHE A 27 TRP 0.007 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2986) covalent geometry : angle 0.70215 ( 4059) hydrogen bonds : bond 0.03062 ( 207) hydrogen bonds : angle 4.15248 ( 606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.085 Fit side-chains REVERT: A 148 PHE cc_start: 0.6344 (m-10) cc_final: 0.4909 (t80) REVERT: A 169 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.4940 (mtt) REVERT: A 359 LEU cc_start: 0.6710 (mt) cc_final: 0.6290 (mp) REVERT: A 365 MET cc_start: 0.5857 (mmm) cc_final: 0.5202 (mmm) REVERT: A 389 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5253 (t80) outliers start: 15 outliers final: 8 residues processed: 60 average time/residue: 0.0447 time to fit residues: 3.5946 Evaluate side-chains 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 14 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 overall best weight: 0.2496 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.211295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.189136 restraints weight = 3806.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.192161 restraints weight = 2660.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.194478 restraints weight = 2062.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.196119 restraints weight = 1706.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.197388 restraints weight = 1469.186| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2986 Z= 0.119 Angle : 0.725 13.143 4059 Z= 0.323 Chirality : 0.041 0.152 483 Planarity : 0.005 0.038 497 Dihedral : 5.083 44.724 409 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.17 % Allowed : 20.51 % Favored : 75.32 % 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 aren not related in a simple way. whole: 0.19 (0.44), residues: 383 helix: 0.63 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.59 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.005 0.001 TYR A 243 PHE 0.008 0.001 PHE A 27 TRP 0.007 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2986) covalent geometry : angle 0.72506 ( 4059) hydrogen bonds : bond 0.02896 ( 207) hydrogen bonds : angle 4.10840 ( 606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.119 Fit side-chains REVERT: A 148 PHE cc_start: 0.6331 (m-10) cc_final: 0.4973 (t80) REVERT: A 169 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.4900 (mtt) REVERT: A 359 LEU cc_start: 0.6678 (mt) cc_final: 0.6283 (mp) REVERT: A 365 MET cc_start: 0.5785 (mmm) cc_final: 0.5142 (mmm) REVERT: A 389 PHE cc_start: 0.6156 (OUTLIER) cc_final: 0.5379 (t80) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.0487 time to fit residues: 3.7123 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.209976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.187529 restraints weight = 3758.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190497 restraints weight = 2682.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192795 restraints weight = 2103.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.194313 restraints weight = 1750.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.194314 restraints weight = 1525.924| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2986 Z= 0.131 Angle : 0.763 12.491 4059 Z= 0.347 Chirality : 0.042 0.193 483 Planarity : 0.006 0.042 497 Dihedral : 5.130 45.458 409 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.17 % Allowed : 22.12 % Favored : 73.72 % 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 aren not related in a simple way. whole: 0.17 (0.44), residues: 383 helix: 0.61 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.51 (0.71), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.023 0.001 TYR A 243 PHE 0.009 0.001 PHE A 27 TRP 0.008 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2986) covalent geometry : angle 0.76287 ( 4059) hydrogen bonds : bond 0.03012 ( 207) hydrogen bonds : angle 4.08309 ( 606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.082 Fit side-chains REVERT: A 148 PHE cc_start: 0.6352 (m-10) cc_final: 0.5003 (t80) REVERT: A 169 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.4977 (mtt) REVERT: A 389 PHE cc_start: 0.6082 (OUTLIER) cc_final: 0.5325 (t80) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.0349 time to fit residues: 2.7111 Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.209282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.187352 restraints weight = 3710.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.189874 restraints weight = 2711.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.192268 restraints weight = 2162.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.193095 restraints weight = 1814.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.194202 restraints weight = 1641.098| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2986 Z= 0.133 Angle : 0.766 11.981 4059 Z= 0.349 Chirality : 0.043 0.178 483 Planarity : 0.006 0.046 497 Dihedral : 5.202 47.448 409 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.85 % Allowed : 22.44 % Favored : 73.72 % 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 aren not related in a simple way. whole: 0.15 (0.44), residues: 383 helix: 0.59 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.52 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 357 TYR 0.018 0.001 TYR A 243 PHE 0.009 0.001 PHE A 27 TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2986) covalent geometry : angle 0.76593 ( 4059) hydrogen bonds : bond 0.03086 ( 207) hydrogen bonds : angle 4.14334 ( 606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 774.37 seconds wall clock time: 13 minutes 58.41 seconds (838.41 seconds total)