Starting phenix.real_space_refine on Tue Feb 3 15:22:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktu_62566/02_2026/9ktu_62566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktu_62566/02_2026/9ktu_62566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ktu_62566/02_2026/9ktu_62566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktu_62566/02_2026/9ktu_62566.map" model { file = "/net/cci-nas-00/data/ceres_data/9ktu_62566/02_2026/9ktu_62566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktu_62566/02_2026/9ktu_62566.cif" } resolution = 3.2 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= 0.026 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 32 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2823 2.51 5 N 634 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 4212 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4199 Classifications: {'peptide': 529} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BAL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2, 'water': 5} Link IDs: {None: 6} Time building chain proxies: 1.13, per 1000 atoms: 0.27 Number of scatterers: 4212 At special positions: 0 Unit cell: (76.38, 66.33, 87.77, 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 32 16.00 Na 1 11.00 O 721 8.00 N 634 7.00 C 2823 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 158.1 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL A 701 " Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 79.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.514A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.625A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 117 removed outlier: 4.027A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) 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 152 removed outlier: 3.697A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 219 through 236 Processing helix chain 'A' and resid 246 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.986A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.155A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.901A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.890A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.777A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.650A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.729A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 4.163A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.051A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.543A pdb=" N VAL A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 474 " --> pdb=" O TRP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.637A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.007A 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 sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 277 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: 0.72 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1221 1.34 - 1.46: 1188 1.46 - 1.58: 1887 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4342 Sorted by residual: bond pdb=" N GLU A 584 " pdb=" CA GLU A 584 " ideal model delta sigma weight residual 1.460 1.441 0.018 1.29e-02 6.01e+03 2.03e+00 bond pdb=" CA GLU A 584 " pdb=" C GLU A 584 " ideal model delta sigma weight residual 1.522 1.513 0.009 8.40e-03 1.42e+04 1.22e+00 bond pdb=" C GLU A 584 " pdb=" O GLU A 584 " ideal model delta sigma weight residual 1.248 1.235 0.013 1.26e-02 6.30e+03 1.08e+00 bond pdb=" C BAL A 701 " pdb=" O BAL A 701 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.31e-01 bond pdb=" CG PRO A 367 " pdb=" CD PRO A 367 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.03e-01 ... (remaining 4337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 5693 1.06 - 2.11: 173 2.11 - 3.17: 44 3.17 - 4.22: 7 4.22 - 5.28: 6 Bond angle restraints: 5923 Sorted by residual: angle pdb=" C BAL A 701 " pdb=" CA BAL A 701 " pdb=" CB BAL A 701 " ideal model delta sigma weight residual 110.50 114.55 -4.05 1.50e+00 4.44e-01 7.30e+00 angle pdb=" N BAL A 701 " pdb=" CB BAL A 701 " pdb=" CA BAL A 701 " ideal model delta sigma weight residual 110.40 113.62 -3.22 1.50e+00 4.44e-01 4.60e+00 angle pdb=" CA GLU A 584 " pdb=" C GLU A 584 " pdb=" O GLU A 584 " ideal model delta sigma weight residual 119.59 121.25 -1.66 7.80e-01 1.64e+00 4.50e+00 angle pdb=" CA GLU A 584 " pdb=" C GLU A 584 " pdb=" N PRO A 585 " ideal model delta sigma weight residual 119.06 116.98 2.08 1.05e+00 9.07e-01 3.91e+00 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.84 122.30 -2.46 1.25e+00 6.40e-01 3.88e+00 ... (remaining 5918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 2287 15.33 - 30.66: 126 30.66 - 46.00: 25 46.00 - 61.33: 7 61.33 - 76.66: 1 Dihedral angle restraints: 2446 sinusoidal: 923 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 150.00 -57.00 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG A 575 " pdb=" CD ARG A 575 " pdb=" NE ARG A 575 " pdb=" CZ ARG A 575 " ideal model delta sinusoidal sigma weight residual -180.00 -137.49 -42.51 2 1.50e+01 4.44e-03 9.74e+00 ... (remaining 2443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 401 0.029 - 0.057: 166 0.057 - 0.086: 52 0.086 - 0.114: 30 0.114 - 0.143: 4 Chirality restraints: 653 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 2.37 0.14 2.00e-01 2.50e+01 5.09e-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 0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" C PRO A 384 " pdb=" CB PRO A 384 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 650 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 129 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C VAL A 129 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 129 " 0.012 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 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C ILE A 130 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE A 130 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 131 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 132 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C SER A 132 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 132 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 133 " 0.009 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 53 2.69 - 3.24: 4359 3.24 - 3.79: 6949 3.79 - 4.35: 9148 4.35 - 4.90: 15723 Nonbonded interactions: 36232 Sorted by model distance: nonbonded pdb=" CD1 LEU A 306 " pdb=" O HOH A 804 " model vdw 2.135 3.460 nonbonded pdb=" NH2 ARG A 41 " pdb=" OD2 ASP A 416 " model vdw 2.246 3.120 nonbonded pdb=" O GLY A 570 " pdb=" NE ARG A 575 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLN A 103 " pdb=" OG SER A 322 " model vdw 2.261 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.293 3.120 ... (remaining 36227 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: 5.500 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 6.160 Find NCS groups from input model: 0.020 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:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 0.023 4343 Z= 0.126 Angle : 0.493 5.281 5925 Z= 0.279 Chirality : 0.039 0.143 653 Planarity : 0.004 0.032 722 Dihedral : 10.346 76.659 1479 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.00 % Allowed : 4.01 % Favored : 93.99 % Cbeta Deviations : 0.21 % 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: 1.06 (0.37), residues: 523 helix: 1.36 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -0.84 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 575 TYR 0.013 0.001 TYR A 69 PHE 0.011 0.001 PHE A 276 TRP 0.008 0.001 TRP A 387 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4342) covalent geometry : angle 0.49267 ( 5923) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.47834 ( 2) hydrogen bonds : bond 0.15676 ( 277) hydrogen bonds : angle 6.57107 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.093 Fit side-chains REVERT: A 211 ASP cc_start: 0.8143 (p0) cc_final: 0.7881 (p0) REVERT: A 247 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: A 452 MET cc_start: 0.8441 (tpp) cc_final: 0.8005 (tpt) REVERT: A 532 TYR cc_start: 0.8681 (t80) cc_final: 0.8191 (t80) outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 0.0415 time to fit residues: 4.3893 Evaluate side-chains 59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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 247 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.137489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.124985 restraints weight = 5047.681| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.45 r_work: 0.3225 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4343 Z= 0.149 Angle : 0.527 5.421 5925 Z= 0.277 Chirality : 0.040 0.140 653 Planarity : 0.004 0.034 722 Dihedral : 5.408 57.114 579 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.90 % Allowed : 7.13 % Favored : 89.98 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.38), residues: 523 helix: 1.80 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.78 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.019 0.001 TYR A 137 PHE 0.016 0.001 PHE A 338 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4342) covalent geometry : angle 0.52709 ( 5923) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.24936 ( 2) hydrogen bonds : bond 0.04600 ( 277) hydrogen bonds : angle 4.69915 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.096 Fit side-chains REVERT: A 176 MET cc_start: 0.7420 (tpp) cc_final: 0.6756 (mpp) REVERT: A 211 ASP cc_start: 0.8517 (p0) cc_final: 0.8298 (p0) REVERT: A 247 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: A 331 CYS cc_start: 0.7741 (m) cc_final: 0.7535 (m) REVERT: A 344 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8048 (mt) REVERT: A 414 LEU cc_start: 0.7555 (mm) cc_final: 0.7256 (mt) REVERT: A 452 MET cc_start: 0.8550 (tpp) cc_final: 0.8148 (tpt) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.0384 time to fit residues: 3.9336 Evaluate side-chains 61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123669 restraints weight = 4977.014| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.46 r_work: 0.3225 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4343 Z= 0.159 Angle : 0.535 8.990 5925 Z= 0.280 Chirality : 0.040 0.164 653 Planarity : 0.004 0.040 722 Dihedral : 5.547 56.779 579 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.45 % Allowed : 10.91 % Favored : 86.64 % Cbeta Deviations : 0.21 % 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: 1.53 (0.38), residues: 523 helix: 1.72 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.86 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.001 TYR A 137 PHE 0.016 0.002 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 4342) covalent geometry : angle 0.53066 ( 5923) SS BOND : bond 0.00849 ( 1) SS BOND : angle 3.82639 ( 2) hydrogen bonds : bond 0.04426 ( 277) hydrogen bonds : angle 4.56846 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.093 Fit side-chains REVERT: A 176 MET cc_start: 0.7417 (tpp) cc_final: 0.6685 (mpp) REVERT: A 211 ASP cc_start: 0.8547 (p0) cc_final: 0.8335 (p0) REVERT: A 344 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 414 LEU cc_start: 0.7548 (mm) cc_final: 0.7274 (mt) REVERT: A 452 MET cc_start: 0.8584 (tpp) cc_final: 0.8113 (tpt) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.0316 time to fit residues: 2.6414 Evaluate side-chains 59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.0670 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.137444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.124661 restraints weight = 4965.710| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.47 r_work: 0.3228 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4343 Z= 0.132 Angle : 0.498 6.931 5925 Z= 0.259 Chirality : 0.039 0.141 653 Planarity : 0.004 0.044 722 Dihedral : 5.240 56.682 577 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.45 % Allowed : 11.36 % Favored : 86.19 % Cbeta Deviations : 0.21 % 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 (0.38), residues: 523 helix: 1.74 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.89 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.015 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4342) covalent geometry : angle 0.49411 ( 5923) SS BOND : bond 0.00272 ( 1) SS BOND : angle 3.23888 ( 2) hydrogen bonds : bond 0.04033 ( 277) hydrogen bonds : angle 4.39829 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.179 Fit side-chains REVERT: A 150 PHE cc_start: 0.8115 (m-10) cc_final: 0.7820 (m-80) REVERT: A 176 MET cc_start: 0.7427 (tpp) cc_final: 0.6697 (mpp) REVERT: A 211 ASP cc_start: 0.8562 (p0) cc_final: 0.8348 (p0) REVERT: A 344 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 414 LEU cc_start: 0.7529 (mm) cc_final: 0.7068 (mm) REVERT: A 452 MET cc_start: 0.8563 (tpp) cc_final: 0.8138 (tpt) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.0488 time to fit residues: 4.5688 Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 32 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125880 restraints weight = 4950.021| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.47 r_work: 0.3246 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4343 Z= 0.115 Angle : 0.477 6.318 5925 Z= 0.249 Chirality : 0.038 0.125 653 Planarity : 0.004 0.045 722 Dihedral : 5.128 56.646 577 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.90 % Allowed : 11.36 % Favored : 85.75 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.37), residues: 523 helix: 1.83 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.95 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.014 0.001 TYR A 138 PHE 0.012 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4342) covalent geometry : angle 0.47409 ( 5923) SS BOND : bond 0.00367 ( 1) SS BOND : angle 2.94565 ( 2) hydrogen bonds : bond 0.03752 ( 277) hydrogen bonds : angle 4.25160 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.093 Fit side-chains REVERT: A 150 PHE cc_start: 0.8115 (m-10) cc_final: 0.7822 (m-80) REVERT: A 176 MET cc_start: 0.7344 (tpp) cc_final: 0.6594 (mpp) REVERT: A 211 ASP cc_start: 0.8556 (p0) cc_final: 0.8353 (p0) REVERT: A 247 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.4708 (m-80) REVERT: A 344 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 414 LEU cc_start: 0.7518 (mm) cc_final: 0.7058 (mm) REVERT: A 426 TYR cc_start: 0.5441 (OUTLIER) cc_final: 0.5146 (t80) REVERT: A 452 MET cc_start: 0.8546 (tpp) cc_final: 0.8077 (tpt) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.0466 time to fit residues: 4.1901 Evaluate side-chains 64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.0020 chunk 41 optimal weight: 0.1980 chunk 7 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127181 restraints weight = 4985.285| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.41 r_work: 0.3259 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4343 Z= 0.108 Angle : 0.468 5.827 5925 Z= 0.244 Chirality : 0.038 0.122 653 Planarity : 0.004 0.044 722 Dihedral : 5.092 56.572 577 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.90 % Allowed : 11.58 % Favored : 85.52 % Cbeta Deviations : 0.21 % 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: 1.73 (0.37), residues: 523 helix: 1.92 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.99 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.013 0.001 TYR A 138 PHE 0.012 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4342) covalent geometry : angle 0.46571 ( 5923) SS BOND : bond 0.00346 ( 1) SS BOND : angle 2.61193 ( 2) hydrogen bonds : bond 0.03653 ( 277) hydrogen bonds : angle 4.19242 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.154 Fit side-chains REVERT: A 150 PHE cc_start: 0.8122 (m-10) cc_final: 0.7836 (m-80) REVERT: A 176 MET cc_start: 0.7275 (tpp) cc_final: 0.6604 (mpp) REVERT: A 211 ASP cc_start: 0.8533 (p0) cc_final: 0.8328 (p0) REVERT: A 247 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.4742 (m-80) REVERT: A 344 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 414 LEU cc_start: 0.7578 (mm) cc_final: 0.7133 (mm) REVERT: A 452 MET cc_start: 0.8540 (tpp) cc_final: 0.8065 (tpt) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0500 time to fit residues: 4.4556 Evaluate side-chains 61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.138258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125225 restraints weight = 5080.274| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.54 r_work: 0.3233 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4343 Z= 0.126 Angle : 0.481 5.869 5925 Z= 0.251 Chirality : 0.039 0.125 653 Planarity : 0.004 0.045 722 Dihedral : 5.114 56.494 577 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.90 % Allowed : 11.58 % Favored : 85.52 % Cbeta Deviations : 0.21 % 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: 1.67 (0.37), residues: 523 helix: 1.88 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4342) covalent geometry : angle 0.47846 ( 5923) SS BOND : bond 0.00330 ( 1) SS BOND : angle 2.76069 ( 2) hydrogen bonds : bond 0.03783 ( 277) hydrogen bonds : angle 4.21835 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.173 Fit side-chains REVERT: A 150 PHE cc_start: 0.8134 (m-10) cc_final: 0.7856 (m-80) REVERT: A 344 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 414 LEU cc_start: 0.7548 (mm) cc_final: 0.7078 (mm) REVERT: A 452 MET cc_start: 0.8559 (tpp) cc_final: 0.8111 (tpt) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.0526 time to fit residues: 4.6663 Evaluate side-chains 64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.136541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123817 restraints weight = 5002.303| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.46 r_work: 0.3215 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4343 Z= 0.151 Angle : 0.503 6.027 5925 Z= 0.263 Chirality : 0.039 0.129 653 Planarity : 0.004 0.045 722 Dihedral : 5.217 56.428 577 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.56 % Allowed : 10.91 % Favored : 85.52 % Cbeta Deviations : 0.21 % 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: 1.57 (0.37), residues: 523 helix: 1.79 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.03 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 201 TYR 0.016 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4342) covalent geometry : angle 0.50059 ( 5923) SS BOND : bond 0.00357 ( 1) SS BOND : angle 2.89817 ( 2) hydrogen bonds : bond 0.04004 ( 277) hydrogen bonds : angle 4.28898 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.089 Fit side-chains REVERT: A 150 PHE cc_start: 0.8095 (m-10) cc_final: 0.7800 (m-80) REVERT: A 176 MET cc_start: 0.7347 (tpp) cc_final: 0.6730 (mpp) REVERT: A 344 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 414 LEU cc_start: 0.7555 (mm) cc_final: 0.7082 (mm) REVERT: A 452 MET cc_start: 0.8570 (tpp) cc_final: 0.8163 (tpt) outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.0319 time to fit residues: 2.8126 Evaluate side-chains 64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.125406 restraints weight = 5061.210| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.51 r_work: 0.3224 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4343 Z= 0.123 Angle : 0.483 5.736 5925 Z= 0.252 Chirality : 0.038 0.123 653 Planarity : 0.004 0.045 722 Dihedral : 5.135 56.128 577 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.34 % Allowed : 11.36 % Favored : 85.30 % Cbeta Deviations : 0.21 % 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: 1.66 (0.37), residues: 523 helix: 1.87 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.03 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4342) covalent geometry : angle 0.48030 ( 5923) SS BOND : bond 0.00314 ( 1) SS BOND : angle 2.81095 ( 2) hydrogen bonds : bond 0.03767 ( 277) hydrogen bonds : angle 4.20977 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.090 Fit side-chains REVERT: A 150 PHE cc_start: 0.8079 (m-10) cc_final: 0.7803 (m-80) REVERT: A 176 MET cc_start: 0.7319 (tpp) cc_final: 0.6686 (mpp) REVERT: A 344 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 414 LEU cc_start: 0.7508 (mm) cc_final: 0.7033 (mm) REVERT: A 426 TYR cc_start: 0.5450 (OUTLIER) cc_final: 0.5129 (t80) REVERT: A 452 MET cc_start: 0.8557 (tpp) cc_final: 0.8141 (tpt) outliers start: 15 outliers final: 12 residues processed: 63 average time/residue: 0.0363 time to fit residues: 3.1674 Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.0070 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.139609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126780 restraints weight = 4941.076| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.49 r_work: 0.3240 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4343 Z= 0.116 Angle : 0.485 5.526 5925 Z= 0.255 Chirality : 0.038 0.121 653 Planarity : 0.004 0.046 722 Dihedral : 5.094 56.133 577 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.90 % Allowed : 11.80 % Favored : 85.30 % Cbeta Deviations : 0.21 % 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: 1.71 (0.37), residues: 523 helix: 1.92 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.05 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 201 TYR 0.013 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4342) covalent geometry : angle 0.48271 ( 5923) SS BOND : bond 0.00314 ( 1) SS BOND : angle 2.61294 ( 2) hydrogen bonds : bond 0.03662 ( 277) hydrogen bonds : angle 4.17016 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.102 Fit side-chains REVERT: A 150 PHE cc_start: 0.8089 (m-10) cc_final: 0.7813 (m-80) REVERT: A 176 MET cc_start: 0.7318 (tpp) cc_final: 0.6673 (mpp) REVERT: A 344 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 452 MET cc_start: 0.8543 (tpp) cc_final: 0.8080 (tpt) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0330 time to fit residues: 2.8578 Evaluate side-chains 62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.138509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.125342 restraints weight = 4991.371| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.53 r_work: 0.3218 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4343 Z= 0.133 Angle : 0.501 6.458 5925 Z= 0.263 Chirality : 0.039 0.125 653 Planarity : 0.004 0.045 722 Dihedral : 5.148 56.186 577 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.56 % Allowed : 11.58 % Favored : 84.86 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.37), residues: 523 helix: 1.86 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4342) covalent geometry : angle 0.49811 ( 5923) SS BOND : bond 0.00355 ( 1) SS BOND : angle 2.89239 ( 2) hydrogen bonds : bond 0.03787 ( 277) hydrogen bonds : angle 4.21654 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 992.04 seconds wall clock time: 17 minutes 45.19 seconds (1065.19 seconds total)