Starting phenix.real_space_refine on Tue Feb 3 15:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktt_62565/02_2026/9ktt_62565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktt_62565/02_2026/9ktt_62565.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/9ktt_62565/02_2026/9ktt_62565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktt_62565/02_2026/9ktt_62565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ktt_62565/02_2026/9ktt_62565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktt_62565/02_2026/9ktt_62565.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= 0.000 sd= 0.024 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2899 2.51 5 N 649 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4335 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4318 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 28, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 17 Unusual residues: {' CL': 1, ' NA': 1, 'TAU': 1} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} Time building chain proxies: 0.95, per 1000 atoms: 0.22 Number of scatterers: 4335 At special positions: 0 Unit cell: (85.76, 69.68, 88.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 1 11.00 O 752 8.00 N 649 7.00 C 2899 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 271.8 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: 1000 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 79.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.798A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.918A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.807A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.269A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.759A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 251 through 267 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.892A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.945A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.001A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.532A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.779A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.512A pdb=" N ARG A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 3.793A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.559A pdb=" N MET A 446 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 449 No H-bonds generated for 'chain 'A' and resid 448 through 449' Processing helix chain 'A' and resid 450 through 461 removed outlier: 4.271A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.505A pdb=" N VAL A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) 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 555 removed outlier: 3.949A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 586 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 276 hydrogen bonds defined for protein. 813 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: 0.45 Time building geometry restraints manager: 0.50 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: 1255 1.35 - 1.46: 1280 1.46 - 1.58: 1885 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4467 Sorted by residual: bond pdb=" O2 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.477 1.545 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O3 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.478 1.433 0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" O1 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.477 1.434 0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" C2 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.801 1.770 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C PHE A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.47e+00 ... (remaining 4462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 5894 1.15 - 2.30: 170 2.30 - 3.44: 29 3.44 - 4.59: 5 4.59 - 5.74: 5 Bond angle restraints: 6103 Sorted by residual: angle pdb=" C GLY A 57 " pdb=" N PHE A 58 " pdb=" CA PHE A 58 " ideal model delta sigma weight residual 122.67 119.26 3.41 1.59e+00 3.96e-01 4.60e+00 angle pdb=" N LYS A 47 " pdb=" CA LYS A 47 " pdb=" CB LYS A 47 " ideal model delta sigma weight residual 113.65 110.62 3.03 1.47e+00 4.63e-01 4.26e+00 angle pdb=" O1 TAU A 701 " pdb=" S TAU A 701 " pdb=" O3 TAU A 701 " ideal model delta sigma weight residual 112.91 118.65 -5.74 3.00e+00 1.11e-01 3.66e+00 angle pdb=" CA PRO A 280 " pdb=" C PRO A 280 " pdb=" N ASP A 281 " ideal model delta sigma weight residual 114.74 116.50 -1.76 1.03e+00 9.43e-01 2.92e+00 angle pdb=" N PHE A 421 " pdb=" CA PHE A 421 " pdb=" C PHE A 421 " ideal model delta sigma weight residual 113.43 111.29 2.14 1.26e+00 6.30e-01 2.89e+00 ... (remaining 6098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.52: 2237 10.52 - 21.05: 194 21.05 - 31.57: 46 31.57 - 42.09: 18 42.09 - 52.62: 11 Dihedral angle restraints: 2506 sinusoidal: 926 harmonic: 1580 Sorted by residual: dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N TYR A 69 " pdb=" CA TYR A 69 " pdb=" CB TYR A 69 " pdb=" CG TYR A 69 " ideal model delta sinusoidal sigma weight residual 60.00 112.62 -52.62 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" N ASP A 401 " pdb=" CA ASP A 401 " pdb=" CB ASP A 401 " pdb=" CG ASP A 401 " ideal model delta sinusoidal sigma weight residual -180.00 -129.62 -50.38 3 1.50e+01 4.44e-03 8.89e+00 ... (remaining 2503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 434 0.031 - 0.062: 180 0.062 - 0.093: 41 0.093 - 0.123: 16 0.123 - 0.154: 3 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA PHE A 58 " pdb=" N PHE A 58 " pdb=" C PHE A 58 " pdb=" CB PHE A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 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 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA THR A 512 " pdb=" N THR A 512 " pdb=" C THR A 512 " pdb=" CB THR A 512 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 671 not shown) Planarity restraints: 745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 129 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C VAL A 129 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL A 129 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 130 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 130 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ILE A 130 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 130 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 131 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 208 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.019 5.00e-02 4.00e+02 ... (remaining 742 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 485 2.75 - 3.28: 4495 3.28 - 3.82: 7650 3.82 - 4.36: 8884 4.36 - 4.90: 15558 Nonbonded interactions: 37072 Sorted by model distance: nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 325 " model vdw 2.206 3.040 nonbonded pdb=" CD1 LEU A 306 " pdb=" O HOH A 805 " model vdw 2.246 3.460 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP A 401 " pdb=" O HOH A 801 " model vdw 2.284 3.040 ... (remaining 37067 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: 4.280 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.000 Process input model: 4.630 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.003 0.068 4468 Z= 0.147 Angle : 0.491 5.738 6105 Z= 0.280 Chirality : 0.038 0.154 674 Planarity : 0.004 0.035 745 Dihedral : 9.743 52.615 1503 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 3.51 % Favored : 94.30 % 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: 0.86 (0.37), residues: 543 helix: 1.14 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.68 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.013 0.001 TYR A 69 PHE 0.010 0.001 PHE A 95 TRP 0.009 0.001 TRP A 113 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4467) covalent geometry : angle 0.49061 ( 6103) SS BOND : bond 0.00232 ( 1) SS BOND : angle 1.13577 ( 2) hydrogen bonds : bond 0.16615 ( 276) hydrogen bonds : angle 6.79296 ( 813) *********************** 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 96 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 212 HIS cc_start: 0.7752 (m90) cc_final: 0.7535 (m90) REVERT: A 275 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7852 (ttmm) REVERT: A 311 SER cc_start: 0.8691 (t) cc_final: 0.8401 (m) REVERT: A 534 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8095 (mtmm) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.0528 time to fit residues: 6.6945 Evaluate side-chains 81 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 467 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.139612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125069 restraints weight = 5306.445| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.33 r_work: 0.3218 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4468 Z= 0.169 Angle : 0.522 5.866 6105 Z= 0.274 Chirality : 0.041 0.159 674 Planarity : 0.005 0.040 745 Dihedral : 5.994 58.322 603 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.17 % Allowed : 7.46 % Favored : 88.38 % 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: 1.21 (0.36), residues: 543 helix: 1.37 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.60 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 324 TYR 0.014 0.002 TYR A 69 PHE 0.013 0.001 PHE A 345 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4467) covalent geometry : angle 0.52038 ( 6103) SS BOND : bond 0.00509 ( 1) SS BOND : angle 2.04038 ( 2) hydrogen bonds : bond 0.04618 ( 276) hydrogen bonds : angle 4.64046 ( 813) *********************** 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 99 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7171 (t80) REVERT: A 190 ASN cc_start: 0.8216 (m110) cc_final: 0.7923 (m-40) REVERT: A 222 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7502 (mp) REVERT: A 275 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7753 (ttmm) REVERT: A 311 SER cc_start: 0.8928 (t) cc_final: 0.8642 (m) REVERT: A 449 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6783 (mm-30) REVERT: A 534 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8103 (mtmm) outliers start: 19 outliers final: 14 residues processed: 93 average time/residue: 0.0520 time to fit residues: 6.5260 Evaluate side-chains 93 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 493 GLU 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 16 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** 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 = 0.3511 r_free = 0.3511 target = 0.143213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128746 restraints weight = 5211.700| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.35 r_work: 0.3284 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4468 Z= 0.107 Angle : 0.451 5.229 6105 Z= 0.234 Chirality : 0.038 0.139 674 Planarity : 0.004 0.041 745 Dihedral : 5.882 59.511 602 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.95 % Allowed : 9.43 % Favored : 86.62 % 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: 1.55 (0.36), residues: 543 helix: 1.67 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.61 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.012 0.001 TYR A 69 PHE 0.009 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4467) covalent geometry : angle 0.45027 ( 6103) SS BOND : bond 0.00348 ( 1) SS BOND : angle 1.59320 ( 2) hydrogen bonds : bond 0.03695 ( 276) hydrogen bonds : angle 4.28534 ( 813) *********************** 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 94 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7173 (t80) REVERT: A 190 ASN cc_start: 0.8227 (m110) cc_final: 0.7939 (t0) REVERT: A 222 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 275 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7706 (ttmm) REVERT: A 311 SER cc_start: 0.8879 (t) cc_final: 0.8622 (m) REVERT: A 327 MET cc_start: 0.7553 (mmt) cc_final: 0.7271 (mmp) REVERT: A 449 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6744 (mm-30) REVERT: A 534 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8142 (mtmm) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.0622 time to fit residues: 7.2239 Evaluate side-chains 90 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** 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 = 0.3478 r_free = 0.3478 target = 0.140622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.126117 restraints weight = 5209.037| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.32 r_work: 0.3244 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4468 Z= 0.136 Angle : 0.474 5.498 6105 Z= 0.245 Chirality : 0.039 0.149 674 Planarity : 0.004 0.039 745 Dihedral : 6.081 59.808 602 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.61 % Allowed : 8.99 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.36), residues: 543 helix: 1.60 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.62 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 95 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4467) covalent geometry : angle 0.47349 ( 6103) SS BOND : bond 0.00409 ( 1) SS BOND : angle 1.65142 ( 2) hydrogen bonds : bond 0.03818 ( 276) hydrogen bonds : angle 4.24799 ( 813) *********************** 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 95 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 190 ASN cc_start: 0.8285 (m110) cc_final: 0.7967 (t0) REVERT: A 192 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 222 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7494 (mp) REVERT: A 275 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7704 (ttmm) REVERT: A 311 SER cc_start: 0.8878 (t) cc_final: 0.8640 (m) REVERT: A 327 MET cc_start: 0.7611 (mmt) cc_final: 0.7312 (mmp) REVERT: A 449 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6713 (mm-30) REVERT: A 534 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8167 (mtmm) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.0600 time to fit residues: 6.9538 Evaluate side-chains 91 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3472 r_free = 0.3472 target = 0.140044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.125691 restraints weight = 5254.088| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.30 r_work: 0.3231 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.134 Angle : 0.473 5.618 6105 Z= 0.244 Chirality : 0.038 0.150 674 Planarity : 0.004 0.038 745 Dihedral : 6.439 59.873 602 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.04 % Allowed : 10.53 % Favored : 84.43 % 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: 1.46 (0.36), residues: 543 helix: 1.58 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.57 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 345 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4467) covalent geometry : angle 0.47228 ( 6103) SS BOND : bond 0.00383 ( 1) SS BOND : angle 1.48491 ( 2) hydrogen bonds : bond 0.03751 ( 276) hydrogen bonds : angle 4.20953 ( 813) *********************** 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 99 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 190 ASN cc_start: 0.8286 (m110) cc_final: 0.7962 (t0) REVERT: A 222 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 226 LEU cc_start: 0.7768 (tp) cc_final: 0.7216 (mt) REVERT: A 275 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7684 (ttmm) REVERT: A 311 SER cc_start: 0.8886 (t) cc_final: 0.8629 (m) REVERT: A 327 MET cc_start: 0.7647 (mmt) cc_final: 0.7332 (mmp) REVERT: A 449 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6691 (mm-30) REVERT: A 534 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8153 (mtmm) outliers start: 23 outliers final: 18 residues processed: 91 average time/residue: 0.0547 time to fit residues: 6.7729 Evaluate side-chains 93 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3470 r_free = 0.3470 target = 0.139726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125291 restraints weight = 5365.236| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.32 r_work: 0.3225 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.135 Angle : 0.474 5.372 6105 Z= 0.245 Chirality : 0.038 0.150 674 Planarity : 0.004 0.037 745 Dihedral : 6.542 59.466 602 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.39 % Allowed : 12.06 % Favored : 83.55 % 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 (0.36), residues: 543 helix: 1.58 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.61 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 392 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4467) covalent geometry : angle 0.47359 ( 6103) SS BOND : bond 0.00370 ( 1) SS BOND : angle 1.43368 ( 2) hydrogen bonds : bond 0.03725 ( 276) hydrogen bonds : angle 4.18856 ( 813) *********************** 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 93 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7276 (t80) REVERT: A 190 ASN cc_start: 0.8309 (m110) cc_final: 0.7967 (t0) REVERT: A 222 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7389 (mp) REVERT: A 226 LEU cc_start: 0.7765 (tp) cc_final: 0.7207 (mt) REVERT: A 275 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7658 (ttmm) REVERT: A 311 SER cc_start: 0.8968 (t) cc_final: 0.8663 (m) REVERT: A 327 MET cc_start: 0.7656 (mmt) cc_final: 0.7398 (mmp) REVERT: A 449 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6630 (mm-30) REVERT: A 534 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8141 (mtmm) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.0622 time to fit residues: 7.2351 Evaluate side-chains 92 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3467 r_free = 0.3467 target = 0.139501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125239 restraints weight = 5275.254| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.32 r_work: 0.3223 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.134 Angle : 0.473 5.371 6105 Z= 0.243 Chirality : 0.038 0.149 674 Planarity : 0.004 0.037 745 Dihedral : 6.004 59.430 600 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.61 % Allowed : 12.50 % Favored : 82.89 % 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 (0.36), residues: 543 helix: 1.55 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.55 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 392 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4467) covalent geometry : angle 0.47216 ( 6103) SS BOND : bond 0.00360 ( 1) SS BOND : angle 1.43151 ( 2) hydrogen bonds : bond 0.03711 ( 276) hydrogen bonds : angle 4.19109 ( 813) *********************** 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 96 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7275 (t80) REVERT: A 190 ASN cc_start: 0.8330 (m110) cc_final: 0.7988 (t0) REVERT: A 222 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 226 LEU cc_start: 0.7772 (tp) cc_final: 0.7209 (mt) REVERT: A 275 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7651 (ttmm) REVERT: A 311 SER cc_start: 0.8970 (t) cc_final: 0.8659 (m) REVERT: A 327 MET cc_start: 0.7687 (mmt) cc_final: 0.7359 (mmp) REVERT: A 449 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6736 (mm-30) REVERT: A 534 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8135 (mtmm) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.0598 time to fit residues: 7.0484 Evaluate side-chains 91 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3494 r_free = 0.3494 target = 0.141725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127460 restraints weight = 5209.005| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.32 r_work: 0.3253 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4468 Z= 0.109 Angle : 0.450 5.277 6105 Z= 0.231 Chirality : 0.037 0.141 674 Planarity : 0.004 0.037 745 Dihedral : 5.664 59.303 599 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.17 % Allowed : 13.16 % Favored : 82.68 % 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: 1.61 (0.36), residues: 543 helix: 1.68 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.50 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.013 0.001 TYR A 69 PHE 0.010 0.001 PHE A 345 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4467) covalent geometry : angle 0.44926 ( 6103) SS BOND : bond 0.00306 ( 1) SS BOND : angle 1.31281 ( 2) hydrogen bonds : bond 0.03470 ( 276) hydrogen bonds : angle 4.12846 ( 813) *********************** 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 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 190 ASN cc_start: 0.8263 (m110) cc_final: 0.7936 (t0) REVERT: A 222 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 275 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7642 (ttmm) REVERT: A 311 SER cc_start: 0.8961 (t) cc_final: 0.8675 (m) REVERT: A 327 MET cc_start: 0.7706 (mmt) cc_final: 0.7382 (mmp) REVERT: A 449 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6666 (mm-30) REVERT: A 534 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8135 (mtmm) outliers start: 19 outliers final: 16 residues processed: 80 average time/residue: 0.0618 time to fit residues: 6.6384 Evaluate side-chains 83 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.0050 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.140762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126596 restraints weight = 5302.660| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.31 r_work: 0.3266 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4468 Z= 0.120 Angle : 0.459 5.293 6105 Z= 0.235 Chirality : 0.038 0.141 674 Planarity : 0.004 0.037 745 Dihedral : 5.569 59.602 599 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.17 % Allowed : 13.38 % Favored : 82.46 % 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: 1.59 (0.36), residues: 543 helix: 1.68 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.53 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.014 0.001 TYR A 69 PHE 0.011 0.001 PHE A 392 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4467) covalent geometry : angle 0.45817 ( 6103) SS BOND : bond 0.00347 ( 1) SS BOND : angle 1.33609 ( 2) hydrogen bonds : bond 0.03548 ( 276) hydrogen bonds : angle 4.12922 ( 813) *********************** 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 88 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7281 (t80) REVERT: A 190 ASN cc_start: 0.8274 (m110) cc_final: 0.7933 (t0) REVERT: A 222 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7432 (mp) REVERT: A 226 LEU cc_start: 0.7765 (tp) cc_final: 0.7201 (mt) REVERT: A 311 SER cc_start: 0.8980 (t) cc_final: 0.8696 (m) REVERT: A 327 MET cc_start: 0.7724 (mmt) cc_final: 0.7384 (mmp) REVERT: A 449 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6712 (mm-30) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.0466 time to fit residues: 5.4099 Evaluate side-chains 85 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.2490 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.143537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129168 restraints weight = 5137.378| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.37 r_work: 0.3279 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4468 Z= 0.096 Angle : 0.457 8.953 6105 Z= 0.229 Chirality : 0.037 0.180 674 Planarity : 0.004 0.037 745 Dihedral : 5.466 59.417 599 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.29 % Allowed : 14.04 % Favored : 82.68 % 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: 1.76 (0.36), residues: 543 helix: 1.81 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.51 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.013 0.001 TYR A 137 PHE 0.009 0.001 PHE A 58 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 4467) covalent geometry : angle 0.45673 ( 6103) SS BOND : bond 0.00295 ( 1) SS BOND : angle 1.26488 ( 2) hydrogen bonds : bond 0.03312 ( 276) hydrogen bonds : angle 4.07395 ( 813) ********************** 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 82 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7137 (t80) REVERT: A 172 MET cc_start: 0.5975 (mtp) cc_final: 0.5659 (mtp) REVERT: A 176 MET cc_start: 0.8053 (tpt) cc_final: 0.7664 (mpp) REVERT: A 190 ASN cc_start: 0.8304 (m110) cc_final: 0.7978 (t0) REVERT: A 222 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7439 (mp) REVERT: A 275 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7592 (ttmm) REVERT: A 311 SER cc_start: 0.8940 (t) cc_final: 0.8676 (m) REVERT: A 327 MET cc_start: 0.7641 (mmt) cc_final: 0.7346 (mmp) REVERT: A 449 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6619 (mm-30) REVERT: A 534 LYS cc_start: 0.8530 (mtmt) cc_final: 0.7864 (pttt) outliers start: 15 outliers final: 13 residues processed: 76 average time/residue: 0.0589 time to fit residues: 5.9893 Evaluate side-chains 82 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.139992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125799 restraints weight = 5275.064| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.33 r_work: 0.3233 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.142 Angle : 0.491 9.029 6105 Z= 0.248 Chirality : 0.039 0.181 674 Planarity : 0.004 0.037 745 Dihedral : 5.515 59.887 599 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.51 % Allowed : 14.04 % Favored : 82.46 % 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: 1.59 (0.36), residues: 543 helix: 1.64 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.44 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 392 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4467) covalent geometry : angle 0.49034 ( 6103) SS BOND : bond 0.00405 ( 1) SS BOND : angle 1.39714 ( 2) hydrogen bonds : bond 0.03696 ( 276) hydrogen bonds : angle 4.15814 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.87 seconds wall clock time: 22 minutes 34.76 seconds (1354.76 seconds total)