Starting phenix.real_space_refine on Wed Jul 1 23:43:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7n_62150/07_2026/9k7n_62150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7n_62150/07_2026/9k7n_62150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k7n_62150/07_2026/9k7n_62150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7n_62150/07_2026/9k7n_62150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k7n_62150/07_2026/9k7n_62150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7n_62150/07_2026/9k7n_62150.map" } resolution = 3.3 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= 0.053 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: 5 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 C 2900 2.51 5 N 658 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4332 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4324 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 518} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 7 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.26, per 1000 atoms: 0.29 Number of scatterers: 4332 At special positions: 0 Unit cell: (81.76, 68.62, 82.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 33 16.00 O 740 8.00 N 658 7.00 C 2900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.05 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: 0.38 Conformation dependent library (CDL) restraints added in 158.9 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 83.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.578A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.726A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.713A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.885A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.953A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.620A pdb=" N GLY A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 245 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.722A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.612A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 287' Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.429A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.535A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.567A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 4.566A pdb=" N PHE A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.960A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.704A pdb=" N GLY A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 3.924A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 448 removed outlier: 3.779A pdb=" N THR A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.654A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 568 removed outlier: 4.025A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 298 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 639 1.31 - 1.44: 1361 1.44 - 1.56: 2424 1.56 - 1.69: 0 1.69 - 1.82: 47 Bond restraints: 4471 Sorted by residual: bond pdb=" C ALA A 78 " pdb=" O ALA A 78 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.24e-02 6.50e+03 1.70e+01 bond pdb=" C LEU A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.22e-02 6.72e+03 7.89e+00 bond pdb=" C TYR A 538 " pdb=" N PRO A 539 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.31e-02 5.83e+03 6.40e+00 bond pdb=" CA SER A 365 " pdb=" C SER A 365 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.20e-02 6.94e+03 5.83e+00 bond pdb=" C VAL A 528 " pdb=" N PRO A 529 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.31e-02 5.83e+03 5.66e+00 ... (remaining 4466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 5849 2.72 - 5.45: 206 5.45 - 8.17: 34 8.17 - 10.90: 9 10.90 - 13.62: 1 Bond angle restraints: 6099 Sorted by residual: angle pdb=" N SER A 121 " pdb=" CA SER A 121 " pdb=" C SER A 121 " ideal model delta sigma weight residual 113.38 103.97 9.41 1.23e+00 6.61e-01 5.85e+01 angle pdb=" N TRP A 65 " pdb=" CA TRP A 65 " pdb=" C TRP A 65 " ideal model delta sigma weight residual 111.14 119.01 -7.87 1.08e+00 8.57e-01 5.31e+01 angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 110.42 117.34 -6.92 9.60e-01 1.09e+00 5.20e+01 angle pdb=" N TYR A 461 " pdb=" CA TYR A 461 " pdb=" C TYR A 461 " ideal model delta sigma weight residual 111.36 119.16 -7.80 1.09e+00 8.42e-01 5.12e+01 angle pdb=" N ARG A 66 " pdb=" CA ARG A 66 " pdb=" C ARG A 66 " ideal model delta sigma weight residual 111.14 118.73 -7.59 1.08e+00 8.57e-01 4.94e+01 ... (remaining 6094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2303 16.01 - 32.03: 167 32.03 - 48.04: 44 48.04 - 64.05: 11 64.05 - 80.07: 2 Dihedral angle restraints: 2527 sinusoidal: 956 harmonic: 1571 Sorted by residual: dihedral pdb=" C TYR A 137 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " pdb=" CB TYR A 137 " ideal model delta harmonic sigma weight residual -122.60 -137.40 14.80 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CA TYR A 137 " pdb=" CB TYR A 137 " ideal model delta harmonic sigma weight residual 122.80 136.78 -13.98 0 2.50e+00 1.60e-01 3.13e+01 dihedral pdb=" C TYR A 461 " pdb=" N TYR A 461 " pdb=" CA TYR A 461 " pdb=" CB TYR A 461 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 2524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 567 0.122 - 0.244: 96 0.244 - 0.366: 8 0.366 - 0.488: 2 0.488 - 0.609: 2 Chirality restraints: 675 Sorted by residual: chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" CA TYR A 461 " pdb=" N TYR A 461 " pdb=" C TYR A 461 " pdb=" CB TYR A 461 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CA PHE A 345 " pdb=" N PHE A 345 " pdb=" C PHE A 345 " pdb=" CB PHE A 345 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 672 not shown) Planarity restraints: 741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 253 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 81 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 82 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 374 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 375 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.039 5.00e-02 4.00e+02 ... (remaining 738 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 54 2.67 - 3.23: 4463 3.23 - 3.79: 7337 3.79 - 4.34: 10113 4.34 - 4.90: 15931 Nonbonded interactions: 37898 Sorted by model distance: nonbonded pdb=" OH TYR A 83 " pdb="CL CL A 702 " model vdw 2.115 3.270 nonbonded pdb=" OD1 ASP A 219 " pdb=" N LEU A 220 " model vdw 2.288 3.120 nonbonded pdb=" N SER A 464 " pdb=" O SER A 464 " model vdw 2.416 2.496 nonbonded pdb=" N SER A 121 " pdb=" N GLY A 122 " model vdw 2.448 2.560 nonbonded pdb=" O PHE A 58 " pdb=" O3 TAU A 701 " model vdw 2.461 3.040 ... (remaining 37893 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 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: 1.810 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.300 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.007 0.051 4472 Z= 0.508 Angle : 1.229 13.622 6101 Z= 0.862 Chirality : 0.094 0.609 675 Planarity : 0.009 0.110 741 Dihedral : 12.281 80.066 1530 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.08 % Allowed : 6.24 % Favored : 92.69 % Cbeta Deviations : 0.20 % 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: 2.30 (0.36), residues: 543 helix: 2.34 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.026 0.002 TYR A 137 PHE 0.020 0.002 PHE A 522 TRP 0.018 0.002 TRP A 387 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.51 ( 4471) covalent geometry : angle 1.22860 / 0.86 ( 6099) SS BOND : bond 0.01563 / 1.04 ( 1) SS BOND : angle 2.12603 / 1.19 ( 2) hydrogen bonds : bond 0.21751 / 14.65 ( 298) hydrogen bonds : angle 7.22434 / 5.23 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8247 (t0) cc_final: 0.7902 (t0) REVERT: A 302 TYR cc_start: 0.7948 (m-80) cc_final: 0.7210 (m-80) REVERT: A 350 PHE cc_start: 0.8349 (t80) cc_final: 0.8039 (t80) REVERT: A 452 MET cc_start: 0.7462 (tpp) cc_final: 0.7236 (tpt) outliers start: 5 outliers final: 3 residues processed: 134 average time/residue: 0.0600 time to fit residues: 10.4989 Evaluate side-chains 78 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 418 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 GLN A 353 GLN A 355 GLN A 456 GLN A 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.176493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146411 restraints weight = 5482.615| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.38 r_work: 0.3646 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4472 Z= 0.171 Angle : 0.665 9.191 6101 Z= 0.355 Chirality : 0.044 0.191 675 Planarity : 0.006 0.060 741 Dihedral : 6.156 59.314 599 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.15 % Allowed : 12.04 % Favored : 85.81 % 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: 1.65 (0.35), residues: 543 helix: 1.74 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -0.54 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.024 0.002 TYR A 498 PHE 0.033 0.002 PHE A 58 TRP 0.016 0.002 TRP A 113 HIS 0.006 0.003 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 4471) covalent geometry : angle 0.66135 / 0.35 ( 6099) SS BOND : bond 0.00548 / 0.37 ( 1) SS BOND : angle 3.71600 / 2.61 ( 2) hydrogen bonds : bond 0.06251 / 4.25 ( 298) hydrogen bonds : angle 5.35831 / 4.00 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.159 Fit side-chains REVERT: A 47 LYS cc_start: 0.7608 (mmtp) cc_final: 0.7350 (pttt) REVERT: A 202 ASN cc_start: 0.8591 (t0) cc_final: 0.8304 (t0) REVERT: A 256 MET cc_start: 0.7702 (tpp) cc_final: 0.7302 (tpt) REVERT: A 302 TYR cc_start: 0.8593 (m-80) cc_final: 0.8129 (m-80) REVERT: A 324 ARG cc_start: 0.6035 (ttp-170) cc_final: 0.5615 (mmp-170) REVERT: A 350 PHE cc_start: 0.8497 (t80) cc_final: 0.8106 (t80) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.0448 time to fit residues: 6.1703 Evaluate side-chains 89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 74 ASN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.176544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146235 restraints weight = 5371.138| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.37 r_work: 0.3622 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4472 Z= 0.150 Angle : 0.595 11.031 6101 Z= 0.308 Chirality : 0.040 0.123 675 Planarity : 0.005 0.058 741 Dihedral : 5.879 59.642 597 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.01 % Allowed : 13.55 % Favored : 83.44 % 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: 1.54 (0.35), residues: 543 helix: 1.60 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -0.46 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 263 TYR 0.018 0.001 TYR A 69 PHE 0.041 0.002 PHE A 58 TRP 0.010 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4471) covalent geometry : angle 0.59380 / 0.31 ( 6099) SS BOND : bond 0.00192 / 0.13 ( 1) SS BOND : angle 1.84006 / 1.31 ( 2) hydrogen bonds : bond 0.05489 / 3.70 ( 298) hydrogen bonds : angle 5.04557 / 3.74 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.155 Fit side-chains REVERT: A 47 LYS cc_start: 0.7614 (mmtp) cc_final: 0.7408 (pttt) REVERT: A 202 ASN cc_start: 0.8599 (t0) cc_final: 0.8307 (t0) REVERT: A 302 TYR cc_start: 0.8555 (m-80) cc_final: 0.8195 (m-80) REVERT: A 324 ARG cc_start: 0.6019 (ttp-170) cc_final: 0.5612 (mmp-170) REVERT: A 350 PHE cc_start: 0.8649 (t80) cc_final: 0.8033 (t80) REVERT: A 408 GLU cc_start: 0.7882 (tp30) cc_final: 0.7642 (tp30) REVERT: A 493 GLU cc_start: 0.7192 (pt0) cc_final: 0.6854 (pt0) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.0429 time to fit residues: 5.4912 Evaluate side-chains 85 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 151 GLN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.174126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143763 restraints weight = 5349.469| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.36 r_work: 0.3593 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4472 Z= 0.144 Angle : 0.558 8.222 6101 Z= 0.290 Chirality : 0.039 0.166 675 Planarity : 0.005 0.055 741 Dihedral : 5.870 59.656 597 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.44 % Allowed : 12.69 % Favored : 83.87 % 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: 1.56 (0.35), residues: 543 helix: 1.59 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -0.45 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.019 0.001 TYR A 69 PHE 0.025 0.002 PHE A 58 TRP 0.011 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 4471) covalent geometry : angle 0.55723 / 0.29 ( 6099) SS BOND : bond 0.00764 / 0.51 ( 1) SS BOND : angle 1.85876 / 1.25 ( 2) hydrogen bonds : bond 0.04978 / 3.33 ( 298) hydrogen bonds : angle 4.82698 / 3.56 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.162 Fit side-chains REVERT: A 202 ASN cc_start: 0.8623 (t0) cc_final: 0.8294 (t0) REVERT: A 302 TYR cc_start: 0.8587 (m-80) cc_final: 0.8282 (m-80) REVERT: A 324 ARG cc_start: 0.6053 (ttp-170) cc_final: 0.5664 (mmp-170) REVERT: A 350 PHE cc_start: 0.8450 (t80) cc_final: 0.8117 (t80) REVERT: A 408 GLU cc_start: 0.7915 (tp30) cc_final: 0.7643 (tp30) outliers start: 16 outliers final: 11 residues processed: 85 average time/residue: 0.0504 time to fit residues: 5.9824 Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.172522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141399 restraints weight = 5520.289| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.39 r_work: 0.3578 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4472 Z= 0.136 Angle : 0.539 7.424 6101 Z= 0.279 Chirality : 0.039 0.193 675 Planarity : 0.005 0.052 741 Dihedral : 5.861 59.860 597 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.01 % Allowed : 15.48 % Favored : 81.51 % 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: 1.63 (0.35), residues: 543 helix: 1.65 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.55 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 564 TYR 0.018 0.001 TYR A 69 PHE 0.038 0.002 PHE A 58 TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4471) covalent geometry : angle 0.53824 / 0.28 ( 6099) SS BOND : bond 0.00261 / 0.17 ( 1) SS BOND : angle 1.70568 / 1.09 ( 2) hydrogen bonds : bond 0.04738 / 3.19 ( 298) hydrogen bonds : angle 4.74128 / 3.48 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8623 (m-80) cc_final: 0.8259 (m-80) REVERT: A 324 ARG cc_start: 0.6079 (ttp-170) cc_final: 0.5676 (mmp-170) REVERT: A 350 PHE cc_start: 0.8497 (t80) cc_final: 0.8150 (t80) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.0488 time to fit residues: 5.5998 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140385 restraints weight = 5623.048| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.39 r_work: 0.3561 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4472 Z= 0.151 Angle : 0.552 7.457 6101 Z= 0.284 Chirality : 0.039 0.191 675 Planarity : 0.005 0.050 741 Dihedral : 5.862 58.705 597 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 16.99 % Favored : 80.43 % 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: 1.62 (0.35), residues: 543 helix: 1.66 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.63 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.019 0.001 TYR A 69 PHE 0.029 0.002 PHE A 58 TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 4471) covalent geometry : angle 0.55115 / 0.28 ( 6099) SS BOND : bond 0.00515 / 0.34 ( 1) SS BOND : angle 1.67489 / 1.13 ( 2) hydrogen bonds : bond 0.04633 / 3.11 ( 298) hydrogen bonds : angle 4.74701 / 3.46 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8683 (m-80) cc_final: 0.8237 (m-80) REVERT: A 324 ARG cc_start: 0.6098 (ttp-170) cc_final: 0.5677 (mmp-170) REVERT: A 408 GLU cc_start: 0.7892 (tp30) cc_final: 0.7658 (tp30) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.0516 time to fit residues: 5.7158 Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139939 restraints weight = 5619.928| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.40 r_work: 0.3556 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4472 Z= 0.147 Angle : 0.546 7.205 6101 Z= 0.281 Chirality : 0.039 0.178 675 Planarity : 0.004 0.046 741 Dihedral : 5.842 58.122 597 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.44 % Allowed : 17.20 % Favored : 79.35 % 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: 1.64 (0.36), residues: 543 helix: 1.71 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.72 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.019 0.001 TYR A 69 PHE 0.030 0.002 PHE A 232 TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4471) covalent geometry : angle 0.54538 / 0.28 ( 6099) SS BOND : bond 0.00209 / 0.14 ( 1) SS BOND : angle 1.53865 / 1.04 ( 2) hydrogen bonds : bond 0.04566 / 3.07 ( 298) hydrogen bonds : angle 4.64467 / 3.39 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.169 Fit side-chains REVERT: A 302 TYR cc_start: 0.8719 (m-80) cc_final: 0.8219 (m-80) REVERT: A 324 ARG cc_start: 0.6074 (ttp-170) cc_final: 0.5610 (mmp-170) REVERT: A 350 PHE cc_start: 0.8569 (t80) cc_final: 0.8245 (t80) REVERT: A 408 GLU cc_start: 0.7903 (tp30) cc_final: 0.7660 (tp30) outliers start: 16 outliers final: 14 residues processed: 86 average time/residue: 0.0506 time to fit residues: 6.0187 Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140999 restraints weight = 5516.501| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.38 r_work: 0.3568 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4472 Z= 0.137 Angle : 0.537 7.123 6101 Z= 0.278 Chirality : 0.038 0.195 675 Planarity : 0.004 0.045 741 Dihedral : 5.806 56.579 597 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.44 % Allowed : 17.42 % Favored : 79.14 % 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: 1.72 (0.35), residues: 543 helix: 1.74 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -0.68 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.018 0.001 TYR A 69 PHE 0.033 0.002 PHE A 232 TRP 0.008 0.001 TRP A 113 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 4471) covalent geometry : angle 0.53644 / 0.28 ( 6099) SS BOND : bond 0.00196 / 0.13 ( 1) SS BOND : angle 1.64101 / 1.13 ( 2) hydrogen bonds : bond 0.04400 / 2.95 ( 298) hydrogen bonds : angle 4.58034 / 3.33 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.156 Fit side-chains REVERT: A 302 TYR cc_start: 0.8719 (m-80) cc_final: 0.8186 (m-80) REVERT: A 324 ARG cc_start: 0.6092 (ttp-170) cc_final: 0.5541 (mmp-170) REVERT: A 350 PHE cc_start: 0.8541 (t80) cc_final: 0.8177 (t80) REVERT: A 408 GLU cc_start: 0.7899 (tp30) cc_final: 0.7645 (tp30) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.0511 time to fit residues: 5.8207 Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136231 restraints weight = 5611.244| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.37 r_work: 0.3508 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4472 Z= 0.195 Angle : 0.612 7.427 6101 Z= 0.314 Chirality : 0.041 0.189 675 Planarity : 0.005 0.045 741 Dihedral : 5.925 57.669 597 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.23 % Allowed : 18.28 % Favored : 78.49 % 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: 1.44 (0.35), residues: 543 helix: 1.58 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -0.98 (0.49), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.023 0.001 TYR A 69 PHE 0.031 0.002 PHE A 232 TRP 0.012 0.001 TRP A 387 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 4471) covalent geometry : angle 0.61143 / 0.31 ( 6099) SS BOND : bond 0.00170 / 0.11 ( 1) SS BOND : angle 1.78480 / 1.24 ( 2) hydrogen bonds : bond 0.04765 / 3.17 ( 298) hydrogen bonds : angle 4.65065 / 3.38 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.161 Fit side-chains REVERT: A 302 TYR cc_start: 0.8855 (m-80) cc_final: 0.8192 (m-80) REVERT: A 324 ARG cc_start: 0.6072 (ttp-170) cc_final: 0.5601 (mmp-170) outliers start: 15 outliers final: 14 residues processed: 78 average time/residue: 0.0545 time to fit residues: 5.9336 Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139022 restraints weight = 5545.638| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.36 r_work: 0.3549 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4472 Z= 0.144 Angle : 0.557 7.178 6101 Z= 0.288 Chirality : 0.039 0.205 675 Planarity : 0.004 0.045 741 Dihedral : 5.833 56.747 597 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 19.57 % Favored : 77.85 % 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: 1.54 (0.35), residues: 543 helix: 1.67 (0.25), residues: 407 sheet: None (None), residues: 0 loop : -0.91 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.021 0.001 TYR A 440 PHE 0.036 0.002 PHE A 232 TRP 0.012 0.001 TRP A 166 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4471) covalent geometry : angle 0.55574 / 0.29 ( 6099) SS BOND : bond 0.00352 / 0.23 ( 1) SS BOND : angle 1.75658 / 1.21 ( 2) hydrogen bonds : bond 0.04483 / 3.01 ( 298) hydrogen bonds : angle 4.56232 / 3.31 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.158 Fit side-chains REVERT: A 302 TYR cc_start: 0.8800 (m-80) cc_final: 0.8121 (m-80) REVERT: A 324 ARG cc_start: 0.5996 (ttp-170) cc_final: 0.5495 (mmp-170) REVERT: A 350 PHE cc_start: 0.8535 (t80) cc_final: 0.8169 (t80) outliers start: 12 outliers final: 12 residues processed: 74 average time/residue: 0.0547 time to fit residues: 5.6030 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140482 restraints weight = 5549.958| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.37 r_work: 0.3564 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4472 Z= 0.137 Angle : 0.563 7.381 6101 Z= 0.290 Chirality : 0.039 0.197 675 Planarity : 0.004 0.046 741 Dihedral : 5.776 56.379 597 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.80 % Allowed : 19.35 % Favored : 77.85 % 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: 1.60 (0.36), residues: 543 helix: 1.71 (0.26), residues: 407 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.020 0.001 TYR A 440 PHE 0.036 0.002 PHE A 232 TRP 0.010 0.001 TRP A 166 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4471) covalent geometry : angle 0.56302 / 0.29 ( 6099) SS BOND : bond 0.00360 / 0.24 ( 1) SS BOND : angle 1.35261 / 0.91 ( 2) hydrogen bonds : bond 0.04354 / 2.93 ( 298) hydrogen bonds : angle 4.52499 / 3.29 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1039.24 seconds wall clock time: 18 minutes 32.86 seconds (1112.86 seconds total)