Starting phenix.real_space_refine on Thu Jul 2 03:40:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dax_46701/07_2026/9dax_46701.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dax_46701/07_2026/9dax_46701.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/9dax_46701/07_2026/9dax_46701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dax_46701/07_2026/9dax_46701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dax_46701/07_2026/9dax_46701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dax_46701/07_2026/9dax_46701.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= 0.050 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 Ca 6 9.91 5 Mg 1 5.21 5 S 26 5.16 5 C 4037 2.51 5 N 1091 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s 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: 6401 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3460 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 26, 'TRANS': 424} Conformer: "B" Number of residues, atoms: 451, 3460 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 26, 'TRANS': 424} bond proxies already assigned to first conformer: 3546 Chain: "B" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2920 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 355} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 7 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 6} Link IDs: {None: 5} Chain breaks: 2 Time building chain proxies: 2.00, per 1000 atoms: 0.31 Number of scatterers: 6401 At special positions: 0 Unit cell: (65.36, 104.06, 84.28, 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) Ca 6 19.99 S 26 16.00 Mg 1 11.99 O 1240 8.00 N 1091 7.00 C 4037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.04 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " 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: 0.50 Conformation dependent library (CDL) restraints added in 531.5 milliseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 14 sheets defined 13.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.524A pdb=" N PHE A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.855A pdb=" N LEU B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 129' Processing helix chain 'B' and resid 133 through 144 removed outlier: 4.032A pdb=" N LYS B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.983A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.811A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.590A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.638A pdb=" N TYR B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.653A pdb=" N ILE A 436 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.537A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA9, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 364 removed outlier: 3.618A pdb=" N ALA A 361 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.368A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE B 88 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 102 Processing sheet with id=AB5, first strand: chain 'B' and resid 194 through 197 removed outlier: 4.164A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 113 " --> pdb=" O SER B 243 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 476 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: 0.90 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 2 1.09 - 1.28: 1084 1.28 - 1.46: 2576 1.46 - 1.65: 2835 1.65 - 1.84: 39 Bond restraints: 6536 Sorted by residual: bond pdb=" CB PRO A 410 " pdb=" CG PRO A 410 " ideal model delta sigma weight residual 1.492 0.899 0.593 5.00e-02 4.00e+02 1.41e+02 bond pdb=" C LYS B 298 " pdb=" O LYS B 298 " ideal model delta sigma weight residual 1.235 1.086 0.149 1.26e-02 6.30e+03 1.40e+02 bond pdb=" N LYS B 298 " pdb=" CA LYS B 298 " ideal model delta sigma weight residual 1.457 1.325 0.132 1.29e-02 6.01e+03 1.05e+02 bond pdb=" CG PRO A 410 " pdb=" CD PRO A 410 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.26e+01 bond pdb=" N LEU B 299 " pdb=" CA LEU B 299 " ideal model delta sigma weight residual 1.456 1.544 -0.088 1.32e-02 5.74e+03 4.43e+01 ... (remaining 6531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.62: 8872 11.62 - 23.23: 6 23.23 - 34.85: 3 34.85 - 46.46: 0 46.46 - 58.08: 1 Bond angle restraints: 8882 Sorted by residual: angle pdb=" N PRO A 410 " pdb=" CD PRO A 410 " pdb=" CG PRO A 410 " ideal model delta sigma weight residual 103.20 75.64 27.56 1.50e+00 4.44e-01 3.38e+02 angle pdb=" CB PRO A 410 " pdb=" CG PRO A 410 " pdb=" CD PRO A 410 " ideal model delta sigma weight residual 106.10 164.18 -58.08 3.20e+00 9.77e-02 3.29e+02 angle pdb=" CA PRO A 410 " pdb=" CB PRO A 410 " pdb=" CG PRO A 410 " ideal model delta sigma weight residual 104.50 70.31 34.19 1.90e+00 2.77e-01 3.24e+02 angle pdb=" N GLU B 297 " pdb=" CA GLU B 297 " pdb=" C GLU B 297 " ideal model delta sigma weight residual 110.80 86.71 24.09 2.13e+00 2.20e-01 1.28e+02 angle pdb=" N LEU B 299 " pdb=" CA LEU B 299 " pdb=" CB LEU B 299 " ideal model delta sigma weight residual 110.53 123.48 -12.95 1.47e+00 4.63e-01 7.76e+01 ... (remaining 8877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 3382 19.35 - 38.69: 398 38.69 - 58.04: 93 58.04 - 77.38: 17 77.38 - 96.73: 9 Dihedral angle restraints: 3899 sinusoidal: 1539 harmonic: 2360 Sorted by residual: dihedral pdb=" N LEU B 299 " pdb=" C LEU B 299 " pdb=" CA LEU B 299 " pdb=" CB LEU B 299 " ideal model delta harmonic sigma weight residual 122.80 155.80 -33.00 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" C LEU B 299 " pdb=" N LEU B 299 " pdb=" CA LEU B 299 " pdb=" CB LEU B 299 " ideal model delta harmonic sigma weight residual -122.60 -152.97 30.37 0 2.50e+00 1.60e-01 1.48e+02 dihedral pdb=" CB CYS A 107 " pdb=" SG CYS A 107 " pdb=" SG CYS A 130 " pdb=" CB CYS A 130 " ideal model delta sinusoidal sigma weight residual 93.00 11.66 81.34 1 1.00e+01 1.00e-02 8.15e+01 ... (remaining 3896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 968 0.283 - 0.565: 2 0.565 - 0.848: 0 0.848 - 1.131: 0 1.131 - 1.414: 1 Chirality restraints: 971 Sorted by residual: chirality pdb=" CA LEU B 299 " pdb=" N LEU B 299 " pdb=" C LEU B 299 " pdb=" CB LEU B 299 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 5.00e+01 chirality pdb=" CA MET B 295 " pdb=" N MET B 295 " pdb=" C MET B 295 " pdb=" CB MET B 295 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA GLU B 297 " pdb=" N GLU B 297 " pdb=" C GLU B 297 " pdb=" CB GLU B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 968 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 110 " 0.071 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO B 111 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 56 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 57 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 294 " 0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LEU B 294 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU B 294 " 0.020 2.00e-02 2.50e+03 pdb=" N MET B 295 " 0.019 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 3 1.71 - 2.51: 105 2.51 - 3.30: 7238 3.30 - 4.10: 15863 4.10 - 4.90: 29247 Warning: very small nonbonded interaction distances. Nonbonded interactions: 52456 Sorted by model distance: nonbonded pdb=" CD1 LEU B 299 " pdb=" CG2 ILE B 304 " model vdw 0.912 3.880 nonbonded pdb=" CD1 LEU B 299 " pdb=" CB ILE B 304 " model vdw 1.453 3.890 nonbonded pdb=" CG LEU B 299 " pdb=" CG2 ILE B 304 " model vdw 1.571 3.890 nonbonded pdb=" CB ILE B 226 " pdb=" CE MET B 295 " model vdw 1.840 3.890 nonbonded pdb=" CG2 ILE B 226 " pdb=" CE MET B 295 " model vdw 1.863 3.880 ... (remaining 52451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 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 : 0.010 0.593 6542 Z= 0.373 Angle : 1.227 58.077 8894 Z= 0.622 Chirality : 0.069 1.414 971 Planarity : 0.007 0.103 1170 Dihedral : 17.643 96.728 2381 Min Nonbonded Distance : 0.912 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.51 % Favored : 95.13 % Rotamer: Outliers : 0.72 % Allowed : 24.89 % Favored : 74.39 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 6.82 % 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: -2.15 (0.28), residues: 822 helix: -1.81 (0.49), residues: 88 sheet: -1.23 (0.31), residues: 252 loop : -1.45 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 261 TYR 0.017 0.001 TYR A 288 PHE 0.019 0.002 PHE B 414 TRP 0.032 0.002 TRP A 260 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00965 / 0.37 ( 6536) covalent geometry : angle 1.22694 / 0.62 ( 8882) SS BOND : bond 0.00502 / 0.24 ( 6) SS BOND : angle 1.24819 / 0.46 ( 12) hydrogen bonds : bond 0.26885 / 17.94 ( 188) hydrogen bonds : angle 10.66624 / 7.29 ( 476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.0867 time to fit residues: 7.0519 Evaluate side-chains 55 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 284 GLN A 333 GLN B 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.240599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.213968 restraints weight = 8150.723| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 1.85 r_work: 0.4412 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4431 r_free = 0.4431 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4431 r_free = 0.4431 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 6542 Z= 0.163 Angle : 0.755 15.825 8894 Z= 0.389 Chirality : 0.047 0.205 971 Planarity : 0.006 0.069 1170 Dihedral : 5.345 37.946 915 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.48 % Favored : 94.15 % Rotamer: Outliers : 2.59 % Allowed : 21.58 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -1.91 (0.28), residues: 822 helix: -1.29 (0.48), residues: 86 sheet: -1.20 (0.31), residues: 258 loop : -1.26 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.021 0.002 TYR A 288 PHE 0.018 0.002 PHE A 356 TRP 0.023 0.002 TRP A 260 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 6536) covalent geometry : angle 0.75437 / 0.39 ( 8882) SS BOND : bond 0.00392 / 0.19 ( 6) SS BOND : angle 1.34149 / 0.47 ( 12) hydrogen bonds : bond 0.04181 / 2.80 ( 188) hydrogen bonds : angle 7.54572 / 5.17 ( 476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 PRO cc_start: 0.7436 (OUTLIER) cc_final: 0.7046 (Cg_exo) REVERT: B 181 LYS cc_start: 0.7550 (mtpp) cc_final: 0.6965 (tppt) REVERT: B 321 TYR cc_start: 0.3189 (OUTLIER) cc_final: 0.2018 (t80) REVERT: B 342 GLN cc_start: 0.6950 (tp40) cc_final: 0.6708 (mm110) outliers start: 18 outliers final: 5 residues processed: 77 average time/residue: 0.0736 time to fit residues: 7.8100 Evaluate side-chains 61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 321 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 333 GLN A 443 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.237070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.221452 restraints weight = 10039.309| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 0.95 r_work: 0.4459 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.4488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 6542 Z= 0.165 Angle : 0.755 16.040 8894 Z= 0.386 Chirality : 0.047 0.185 971 Planarity : 0.006 0.069 1170 Dihedral : 4.948 27.352 904 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.36 % Favored : 94.40 % Rotamer: Outliers : 2.73 % Allowed : 21.73 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.28), residues: 822 helix: -1.40 (0.46), residues: 93 sheet: -1.17 (0.31), residues: 258 loop : -1.36 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.019 0.002 TYR A 380 PHE 0.018 0.002 PHE B 431 TRP 0.023 0.002 TRP A 260 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 6536) covalent geometry : angle 0.75334 / 0.39 ( 8882) SS BOND : bond 0.00497 / 0.24 ( 6) SS BOND : angle 1.51713 / 0.54 ( 12) hydrogen bonds : bond 0.03866 / 2.59 ( 188) hydrogen bonds : angle 7.21375 / 4.93 ( 476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 PRO cc_start: 0.7618 (OUTLIER) cc_final: 0.7216 (Cg_exo) REVERT: A 427 ILE cc_start: 0.4556 (OUTLIER) cc_final: 0.3997 (tt) REVERT: B 181 LYS cc_start: 0.7344 (mtpp) cc_final: 0.7041 (tppt) REVERT: B 321 TYR cc_start: 0.3349 (OUTLIER) cc_final: 0.2268 (t80) outliers start: 19 outliers final: 7 residues processed: 78 average time/residue: 0.0853 time to fit residues: 8.9213 Evaluate side-chains 60 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 134 GLN ** B 82 GLN ** 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 = 0.4804 r_free = 0.4804 target = 0.233470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.201399 restraints weight = 8538.601| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 2.25 r_work: 0.4211 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6542 Z= 0.182 Angle : 0.769 16.055 8894 Z= 0.392 Chirality : 0.048 0.245 971 Planarity : 0.006 0.070 1170 Dihedral : 5.061 27.039 904 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 3.88 % Allowed : 20.86 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -2.00 (0.28), residues: 822 helix: -1.30 (0.47), residues: 91 sheet: -1.16 (0.32), residues: 250 loop : -1.41 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 62 TYR 0.023 0.002 TYR A 288 PHE 0.018 0.002 PHE A 356 TRP 0.016 0.002 TRP A 260 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 6536) covalent geometry : angle 0.76784 / 0.39 ( 8882) SS BOND : bond 0.00490 / 0.24 ( 6) SS BOND : angle 1.50215 / 0.55 ( 12) hydrogen bonds : bond 0.03702 / 2.50 ( 188) hydrogen bonds : angle 7.10739 / 4.89 ( 476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.3598 (OUTLIER) cc_final: 0.3115 (m-10) REVERT: A 288 TYR cc_start: 0.2857 (OUTLIER) cc_final: 0.2345 (t80) REVERT: A 410 PRO cc_start: 0.7306 (OUTLIER) cc_final: 0.6902 (Cg_exo) REVERT: A 427 ILE cc_start: 0.4472 (OUTLIER) cc_final: 0.3858 (tt) REVERT: B 181 LYS cc_start: 0.7675 (mtpp) cc_final: 0.6962 (tppt) REVERT: B 209 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7126 (pttm) REVERT: B 321 TYR cc_start: 0.3909 (OUTLIER) cc_final: 0.2484 (t80) REVERT: B 361 ASP cc_start: 0.6632 (t0) cc_final: 0.6379 (t0) REVERT: B 413 SER cc_start: 0.6888 (OUTLIER) cc_final: 0.6359 (t) outliers start: 27 outliers final: 10 residues processed: 85 average time/residue: 0.0874 time to fit residues: 9.7888 Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 0.0050 chunk 51 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.231496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.202103 restraints weight = 8552.321| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 1.98 r_work: 0.4260 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4269 r_free = 0.4269 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4269 r_free = 0.4269 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.4269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 6542 Z= 0.190 Angle : 0.785 16.021 8894 Z= 0.398 Chirality : 0.049 0.248 971 Planarity : 0.006 0.070 1170 Dihedral : 5.191 28.299 904 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.91 % Rotamer: Outliers : 4.17 % Allowed : 20.58 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -2.09 (0.28), residues: 822 helix: -1.31 (0.50), residues: 91 sheet: -1.18 (0.32), residues: 250 loop : -1.51 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.022 0.002 TYR A 380 PHE 0.019 0.002 PHE A 356 TRP 0.018 0.002 TRP A 260 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 6536) covalent geometry : angle 0.78358 / 0.40 ( 8882) SS BOND : bond 0.00493 / 0.24 ( 6) SS BOND : angle 1.55841 / 0.59 ( 12) hydrogen bonds : bond 0.03633 / 2.46 ( 188) hydrogen bonds : angle 7.13105 / 4.93 ( 476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.3646 (OUTLIER) cc_final: 0.3102 (m-10) REVERT: A 288 TYR cc_start: 0.2419 (OUTLIER) cc_final: 0.2136 (t80) REVERT: A 410 PRO cc_start: 0.7365 (OUTLIER) cc_final: 0.6960 (Cg_exo) REVERT: A 427 ILE cc_start: 0.4585 (OUTLIER) cc_final: 0.4026 (tt) REVERT: B 181 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7062 (tppt) REVERT: B 209 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7197 (pttm) REVERT: B 413 SER cc_start: 0.6690 (OUTLIER) cc_final: 0.6447 (t) outliers start: 29 outliers final: 16 residues processed: 93 average time/residue: 0.0674 time to fit residues: 8.4914 Evaluate side-chains 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 42 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN B 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.233191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.216126 restraints weight = 12155.847| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 1.38 r_work: 0.4323 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4353 r_free = 0.4353 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4353 r_free = 0.4353 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 6542 Z= 0.155 Angle : 0.749 16.100 8894 Z= 0.378 Chirality : 0.047 0.199 971 Planarity : 0.005 0.069 1170 Dihedral : 5.029 32.344 904 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.48 % Favored : 94.28 % Rotamer: Outliers : 3.60 % Allowed : 22.16 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.11 (0.28), residues: 822 helix: -1.33 (0.50), residues: 91 sheet: -1.15 (0.32), residues: 246 loop : -1.55 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.020 0.002 TYR A 380 PHE 0.018 0.002 PHE A 356 TRP 0.013 0.002 TRP A 260 HIS 0.002 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 6536) covalent geometry : angle 0.74782 / 0.38 ( 8882) SS BOND : bond 0.00453 / 0.22 ( 6) SS BOND : angle 1.35904 / 0.50 ( 12) hydrogen bonds : bond 0.03265 / 2.23 ( 188) hydrogen bonds : angle 6.87520 / 4.75 ( 476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: A 204 PHE cc_start: 0.4021 (OUTLIER) cc_final: 0.3488 (m-10) REVERT: A 288 TYR cc_start: 0.2409 (OUTLIER) cc_final: 0.1759 (t80) REVERT: A 410 PRO cc_start: 0.7652 (OUTLIER) cc_final: 0.7251 (Cg_exo) REVERT: A 427 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4485 (tt) REVERT: B 181 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7258 (tppt) REVERT: B 209 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6886 (pttm) outliers start: 25 outliers final: 14 residues processed: 84 average time/residue: 0.0857 time to fit residues: 9.5026 Evaluate side-chains 77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.236455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.218396 restraints weight = 8162.367| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 1.00 r_work: 0.4401 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 6542 Z= 0.125 Angle : 0.706 16.153 8894 Z= 0.357 Chirality : 0.046 0.171 971 Planarity : 0.005 0.066 1170 Dihedral : 4.816 31.635 904 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 2.59 % Allowed : 24.03 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.96 (0.28), residues: 822 helix: -1.24 (0.51), residues: 92 sheet: -1.10 (0.32), residues: 252 loop : -1.40 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.020 0.001 TYR A 380 PHE 0.018 0.001 PHE A 356 TRP 0.009 0.001 TRP B 238 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 6536) covalent geometry : angle 0.70543 / 0.36 ( 8882) SS BOND : bond 0.00415 / 0.20 ( 6) SS BOND : angle 1.17373 / 0.44 ( 12) hydrogen bonds : bond 0.03019 / 2.08 ( 188) hydrogen bonds : angle 6.64533 / 4.57 ( 476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.4050 (OUTLIER) cc_final: 0.3544 (m-10) REVERT: A 288 TYR cc_start: 0.2098 (OUTLIER) cc_final: 0.1503 (t80) REVERT: A 410 PRO cc_start: 0.7546 (OUTLIER) cc_final: 0.7143 (Cg_exo) REVERT: A 427 ILE cc_start: 0.4996 (OUTLIER) cc_final: 0.4414 (tt) REVERT: B 181 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7218 (tppt) outliers start: 18 outliers final: 11 residues processed: 71 average time/residue: 0.0904 time to fit residues: 8.5871 Evaluate side-chains 65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.234694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.202801 restraints weight = 12106.461| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 3.32 r_work: 0.4241 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4280 r_free = 0.4280 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4279 r_free = 0.4279 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 6542 Z= 0.149 Angle : 0.735 16.107 8894 Z= 0.371 Chirality : 0.047 0.174 971 Planarity : 0.005 0.065 1170 Dihedral : 4.895 31.080 904 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 3.17 % Allowed : 23.88 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.98 (0.28), residues: 822 helix: -1.32 (0.49), residues: 97 sheet: -1.09 (0.32), residues: 252 loop : -1.43 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.019 0.002 TYR A 380 PHE 0.017 0.002 PHE A 356 TRP 0.010 0.002 TRP A 260 HIS 0.002 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 6536) covalent geometry : angle 0.73379 / 0.37 ( 8882) SS BOND : bond 0.00451 / 0.22 ( 6) SS BOND : angle 1.32141 / 0.49 ( 12) hydrogen bonds : bond 0.03132 / 2.14 ( 188) hydrogen bonds : angle 6.60150 / 4.56 ( 476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.3654 (OUTLIER) cc_final: 0.3154 (m-10) REVERT: A 288 TYR cc_start: 0.2159 (OUTLIER) cc_final: 0.1601 (t80) REVERT: A 333 GLN cc_start: 0.6642 (pt0) cc_final: 0.6394 (pt0) REVERT: A 410 PRO cc_start: 0.7443 (OUTLIER) cc_final: 0.7027 (Cg_exo) REVERT: A 427 ILE cc_start: 0.4726 (OUTLIER) cc_final: 0.4161 (tt) REVERT: B 118 MET cc_start: 0.5229 (ttm) cc_final: 0.5010 (ttm) REVERT: B 181 LYS cc_start: 0.7652 (mtpp) cc_final: 0.6979 (tppt) outliers start: 22 outliers final: 11 residues processed: 76 average time/residue: 0.0832 time to fit residues: 8.5769 Evaluate side-chains 68 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.232950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.215749 restraints weight = 10124.467| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 1.11 r_work: 0.4350 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4387 r_free = 0.4387 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4387 r_free = 0.4387 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.4387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 6542 Z= 0.161 Angle : 0.755 16.106 8894 Z= 0.380 Chirality : 0.047 0.190 971 Planarity : 0.005 0.069 1170 Dihedral : 5.012 32.152 904 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.33 % Favored : 93.54 % Rotamer: Outliers : 2.59 % Allowed : 24.89 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.95 (0.28), residues: 822 helix: -1.38 (0.49), residues: 97 sheet: -1.02 (0.32), residues: 257 loop : -1.41 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.019 0.002 TYR A 288 PHE 0.019 0.002 PHE A 356 TRP 0.010 0.002 TRP A 110 HIS 0.002 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 6536) covalent geometry : angle 0.75421 / 0.38 ( 8882) SS BOND : bond 0.00476 / 0.23 ( 6) SS BOND : angle 1.39275 / 0.51 ( 12) hydrogen bonds : bond 0.03217 / 2.20 ( 188) hydrogen bonds : angle 6.69929 / 4.63 ( 476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.4127 (OUTLIER) cc_final: 0.3637 (m-10) REVERT: A 288 TYR cc_start: 0.2040 (OUTLIER) cc_final: 0.1823 (t80) REVERT: A 333 GLN cc_start: 0.6989 (pt0) cc_final: 0.6430 (mm-40) REVERT: A 410 PRO cc_start: 0.7604 (OUTLIER) cc_final: 0.7199 (Cg_exo) REVERT: A 427 ILE cc_start: 0.5075 (OUTLIER) cc_final: 0.4530 (tt) REVERT: B 181 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7185 (tppt) outliers start: 18 outliers final: 12 residues processed: 72 average time/residue: 0.0839 time to fit residues: 8.2878 Evaluate side-chains 70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 69 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.234596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.218925 restraints weight = 13227.979| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 1.29 r_work: 0.4402 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 6542 Z= 0.140 Angle : 0.729 16.145 8894 Z= 0.367 Chirality : 0.046 0.178 971 Planarity : 0.005 0.066 1170 Dihedral : 4.877 31.974 904 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 2.45 % Allowed : 24.46 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.88 (0.28), residues: 822 helix: -1.29 (0.50), residues: 97 sheet: -0.98 (0.32), residues: 257 loop : -1.36 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.020 0.002 TYR A 288 PHE 0.018 0.002 PHE A 356 TRP 0.009 0.001 TRP A 260 HIS 0.002 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 6536) covalent geometry : angle 0.72831 / 0.37 ( 8882) SS BOND : bond 0.00440 / 0.21 ( 6) SS BOND : angle 1.25087 / 0.46 ( 12) hydrogen bonds : bond 0.03001 / 2.05 ( 188) hydrogen bonds : angle 6.56355 / 4.53 ( 476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.4202 (OUTLIER) cc_final: 0.3709 (m-10) REVERT: A 288 TYR cc_start: 0.1913 (OUTLIER) cc_final: 0.1692 (t80) REVERT: A 333 GLN cc_start: 0.6954 (pt0) cc_final: 0.6436 (mm-40) REVERT: A 410 PRO cc_start: 0.7601 (OUTLIER) cc_final: 0.7205 (Cg_exo) REVERT: A 427 ILE cc_start: 0.5055 (OUTLIER) cc_final: 0.4514 (tt) REVERT: B 181 LYS cc_start: 0.7440 (mtpp) cc_final: 0.7180 (tppt) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.0848 time to fit residues: 8.3149 Evaluate side-chains 72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 410 PRO Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 11 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.235303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.218743 restraints weight = 12091.531| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 1.36 r_work: 0.4356 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 6542 Z= 0.135 Angle : 0.719 16.144 8894 Z= 0.361 Chirality : 0.046 0.171 971 Planarity : 0.005 0.061 1170 Dihedral : 4.842 31.721 904 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.48 % Favored : 94.40 % Rotamer: Outliers : 2.45 % Allowed : 24.89 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.89 (0.28), residues: 822 helix: -1.36 (0.49), residues: 99 sheet: -1.02 (0.32), residues: 259 loop : -1.33 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.022 0.002 TYR A 288 PHE 0.017 0.002 PHE A 356 TRP 0.011 0.001 TRP B 129 HIS 0.001 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6536) covalent geometry : angle 0.71849 / 0.36 ( 8882) SS BOND : bond 0.00422 / 0.20 ( 6) SS BOND : angle 1.25529 / 0.47 ( 12) hydrogen bonds : bond 0.02940 / 2.01 ( 188) hydrogen bonds : angle 6.47943 / 4.46 ( 476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1608.52 seconds wall clock time: 28 minutes 21.47 seconds (1701.47 seconds total)