Starting phenix.real_space_refine on Wed Mar 4 03:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyj_27080/03_2026/8cyj_27080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyj_27080/03_2026/8cyj_27080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cyj_27080/03_2026/8cyj_27080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyj_27080/03_2026/8cyj_27080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cyj_27080/03_2026/8cyj_27080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyj_27080/03_2026/8cyj_27080.map" } resolution = 3.6 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 3454 2.51 5 N 940 2.21 5 O 1066 1.98 5 H 5089 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10575 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1908 Classifications: {'peptide': 127} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1883 Classifications: {'peptide': 125} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1945 Classifications: {'peptide': 128} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1885 Classifications: {'peptide': 127} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "R" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2954 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 2.01, per 1000 atoms: 0.19 Number of scatterers: 10575 At special positions: 0 Unit cell: (68.552, 107.008, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 1066 8.00 N 940 7.00 C 3454 6.00 H 5089 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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: 1.00 Conformation dependent library (CDL) restraints added in 375.1 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 9.3% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.707A pdb=" N LYS A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.779A pdb=" N THR D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.857A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE R 342 " --> pdb=" O PHE R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 405 through 410 Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.207A pdb=" N GLY A 10 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARG A 38 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.207A pdb=" N GLY A 10 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 101 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 116 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.292A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N SER B 124 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 12 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N TYR B 32 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 52 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.292A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N SER B 124 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 12 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 98 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR B 114 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.923A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.923A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR C 117 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 33 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.832A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 452 through 454 206 hydrogen bonds defined for protein. 474 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: 2.64 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5089 1.03 - 1.23: 0 1.23 - 1.42: 2555 1.42 - 1.62: 3027 1.62 - 1.81: 36 Bond restraints: 10707 Sorted by residual: bond pdb=" CB PRO R 463 " pdb=" CG PRO R 463 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.91e+00 bond pdb=" CG PRO R 463 " pdb=" CD PRO R 463 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" N ILE R 410 " pdb=" CA ILE R 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.19e+00 bond pdb=" CB MET B 78 " pdb=" CG MET B 78 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.70e-01 bond pdb=" CA ASP A 76 " pdb=" C ASP A 76 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.21e-02 6.83e+03 7.62e-01 ... (remaining 10702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 18554 1.38 - 2.75: 471 2.75 - 4.13: 43 4.13 - 5.51: 6 5.51 - 6.88: 2 Bond angle restraints: 19076 Sorted by residual: angle pdb=" C ALA R 475 " pdb=" CA ALA R 475 " pdb=" CB ALA R 475 " ideal model delta sigma weight residual 115.79 109.92 5.87 1.19e+00 7.06e-01 2.44e+01 angle pdb=" N SER R 477 " pdb=" CA SER R 477 " pdb=" C SER R 477 " ideal model delta sigma weight residual 114.75 110.21 4.54 1.26e+00 6.30e-01 1.30e+01 angle pdb=" N ARG B 67 " pdb=" CA ARG B 67 " pdb=" C ARG B 67 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.95e+00 angle pdb=" N ASP C 105 " pdb=" CA ASP C 105 " pdb=" C ASP C 105 " ideal model delta sigma weight residual 107.93 113.04 -5.11 1.65e+00 3.67e-01 9.59e+00 angle pdb=" CA PRO R 463 " pdb=" N PRO R 463 " pdb=" CD PRO R 463 " ideal model delta sigma weight residual 112.00 107.95 4.05 1.40e+00 5.10e-01 8.37e+00 ... (remaining 19071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4694 17.32 - 34.63: 337 34.63 - 51.95: 91 51.95 - 69.27: 31 69.27 - 86.59: 14 Dihedral angle restraints: 5167 sinusoidal: 2693 harmonic: 2474 Sorted by residual: dihedral pdb=" CA HIS C 103 " pdb=" C HIS C 103 " pdb=" N GLU C 104 " pdb=" CA GLU C 104 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA PRO D 108 " pdb=" C PRO D 108 " pdb=" N GLY D 109 " pdb=" CA GLY D 109 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLY D 109 " pdb=" C GLY D 109 " pdb=" N ASN D 110 " pdb=" CA ASN D 110 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 5164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 543 0.035 - 0.070: 174 0.070 - 0.105: 45 0.105 - 0.141: 30 0.141 - 0.176: 1 Chirality restraints: 793 Sorted by residual: chirality pdb=" CA PRO R 463 " pdb=" N PRO R 463 " pdb=" C PRO R 463 " pdb=" CB PRO R 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE R 434 " pdb=" N ILE R 434 " pdb=" C ILE R 434 " pdb=" CB ILE R 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL C 124 " pdb=" N VAL C 124 " pdb=" C VAL C 124 " pdb=" CB VAL C 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 790 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO R 463 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 75 " -0.214 9.50e-02 1.11e+02 7.17e-02 6.21e+00 pdb=" NE ARG A 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 75 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 75 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 75 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 75 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 75 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 75 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 75 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO R 491 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.034 5.00e-02 4.00e+02 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 387 2.15 - 2.77: 19600 2.77 - 3.38: 28501 3.38 - 3.99: 38687 3.99 - 4.60: 58143 Nonbonded interactions: 145318 Sorted by model distance: nonbonded pdb=" OE1 GLN A 119 " pdb=" H GLN A 119 " model vdw 1.543 2.450 nonbonded pdb=" O VAL A 105 " pdb=" HH TYR R 489 " model vdw 1.659 2.450 nonbonded pdb=" O ARG C 31 " pdb=" H HIS C 103 " model vdw 1.703 2.450 nonbonded pdb="HH12 ARG B 38 " pdb=" OE1 GLU B 89 " model vdw 1.710 2.450 nonbonded pdb=" O TYR C 52 " pdb="HH11 ARG C 72 " model vdw 1.714 2.450 ... (remaining 145313 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 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 0.099 5626 Z= 0.132 Angle : 0.619 6.883 7632 Z= 0.375 Chirality : 0.042 0.176 793 Planarity : 0.006 0.131 996 Dihedral : 14.181 86.585 1988 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.66 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.31), residues: 691 helix: -2.74 (0.94), residues: 20 sheet: 0.34 (0.31), residues: 236 loop : -1.07 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 75 TYR 0.006 0.001 TYR D 114 PHE 0.009 0.001 PHE B 29 TRP 0.024 0.001 TRP A 53 HIS 0.001 0.000 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5618) covalent geometry : angle 0.61883 ( 7616) SS BOND : bond 0.00199 ( 8) SS BOND : angle 0.49491 ( 16) hydrogen bonds : bond 0.14285 ( 190) hydrogen bonds : angle 7.37863 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 MET cc_start: 0.7670 (mmm) cc_final: 0.7229 (mmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2094 time to fit residues: 23.7074 Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.118493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.106162 restraints weight = 89326.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.109207 restraints weight = 44137.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.111048 restraints weight = 26973.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.112173 restraints weight = 19179.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.112903 restraints weight = 15084.744| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 5626 Z= 0.167 Angle : 0.583 6.868 7632 Z= 0.319 Chirality : 0.043 0.188 793 Planarity : 0.006 0.128 996 Dihedral : 5.437 32.408 789 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.66 % Favored : 92.47 % Rotamer: Outliers : 1.04 % Allowed : 6.39 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.11 (0.31), residues: 691 helix: -4.50 (0.96), residues: 8 sheet: 0.28 (0.31), residues: 244 loop : -1.32 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 75 TYR 0.015 0.002 TYR D 114 PHE 0.014 0.002 PHE R 377 TRP 0.012 0.001 TRP A 53 HIS 0.003 0.001 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5618) covalent geometry : angle 0.57981 ( 7616) SS BOND : bond 0.00324 ( 8) SS BOND : angle 1.37017 ( 16) hydrogen bonds : bond 0.03472 ( 190) hydrogen bonds : angle 6.30037 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 88 average time/residue: 0.2569 time to fit residues: 26.7219 Evaluate side-chains 84 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.113494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.101006 restraints weight = 90671.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.103909 restraints weight = 45750.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.105696 restraints weight = 28629.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.106773 restraints weight = 20651.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.107465 restraints weight = 16547.246| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 5626 Z= 0.187 Angle : 0.621 6.666 7632 Z= 0.340 Chirality : 0.044 0.194 793 Planarity : 0.006 0.125 996 Dihedral : 5.697 34.416 789 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.96 % Favored : 91.17 % Rotamer: Outliers : 2.76 % Allowed : 8.81 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.29 (0.32), residues: 691 helix: -4.46 (1.04), residues: 8 sheet: 0.10 (0.32), residues: 247 loop : -1.42 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.021 0.002 TYR C 106 PHE 0.019 0.002 PHE R 377 TRP 0.011 0.001 TRP R 436 HIS 0.005 0.003 HIS R 519 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5618) covalent geometry : angle 0.61997 ( 7616) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.11317 ( 16) hydrogen bonds : bond 0.03588 ( 190) hydrogen bonds : angle 6.29220 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 89 average time/residue: 0.2197 time to fit residues: 23.7082 Evaluate side-chains 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.102305 restraints weight = 89934.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.105277 restraints weight = 44985.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.107020 restraints weight = 27860.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.108124 restraints weight = 20047.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.108806 restraints weight = 15967.772| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 5626 Z= 0.123 Angle : 0.544 6.309 7632 Z= 0.293 Chirality : 0.043 0.186 793 Planarity : 0.005 0.123 996 Dihedral : 5.374 32.411 789 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.67 % Favored : 91.46 % Rotamer: Outliers : 1.90 % Allowed : 11.23 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.29 (0.32), residues: 691 helix: -4.19 (1.28), residues: 8 sheet: 0.04 (0.32), residues: 259 loop : -1.42 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.014 0.001 TYR D 114 PHE 0.020 0.002 PHE R 338 TRP 0.010 0.001 TRP R 436 HIS 0.003 0.002 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5618) covalent geometry : angle 0.54399 ( 7616) SS BOND : bond 0.00207 ( 8) SS BOND : angle 0.62830 ( 16) hydrogen bonds : bond 0.02947 ( 190) hydrogen bonds : angle 6.12906 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6474 (m100) cc_final: 0.5447 (m100) outliers start: 11 outliers final: 11 residues processed: 86 average time/residue: 0.2118 time to fit residues: 22.1602 Evaluate side-chains 84 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 HIS C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.110374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.097942 restraints weight = 89861.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.100841 restraints weight = 45872.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.102572 restraints weight = 28672.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.103647 restraints weight = 20775.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.104352 restraints weight = 16650.501| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 5626 Z= 0.209 Angle : 0.616 6.308 7632 Z= 0.339 Chirality : 0.044 0.196 793 Planarity : 0.006 0.122 996 Dihedral : 5.730 34.585 789 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.55 % Favored : 89.58 % Rotamer: Outliers : 3.63 % Allowed : 11.57 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.32), residues: 691 helix: -4.71 (0.79), residues: 8 sheet: -0.07 (0.33), residues: 248 loop : -1.63 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 72 TYR 0.019 0.002 TYR C 106 PHE 0.020 0.002 PHE R 338 TRP 0.013 0.002 TRP R 436 HIS 0.005 0.003 HIS R 519 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5618) covalent geometry : angle 0.61272 ( 7616) SS BOND : bond 0.00338 ( 8) SS BOND : angle 1.54610 ( 16) hydrogen bonds : bond 0.03616 ( 190) hydrogen bonds : angle 6.37761 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.5867 (mmm) cc_final: 0.5296 (mmm) REVERT: D 29 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.6131 (t80) REVERT: R 433 VAL cc_start: 0.5435 (OUTLIER) cc_final: 0.4986 (p) outliers start: 21 outliers final: 17 residues processed: 89 average time/residue: 0.2071 time to fit residues: 22.4875 Evaluate side-chains 93 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.099475 restraints weight = 89709.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.102535 restraints weight = 43909.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.104354 restraints weight = 26855.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.105396 restraints weight = 19164.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.105946 restraints weight = 15418.278| |-----------------------------------------------------------------------------| r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 5626 Z= 0.119 Angle : 0.540 5.952 7632 Z= 0.291 Chirality : 0.043 0.183 793 Planarity : 0.005 0.121 996 Dihedral : 5.387 31.261 789 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.53 % Favored : 91.75 % Rotamer: Outliers : 2.94 % Allowed : 12.61 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.49 (0.32), residues: 691 helix: -4.48 (0.99), residues: 8 sheet: -0.10 (0.32), residues: 264 loop : -1.57 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.010 0.001 TYR B 112 PHE 0.028 0.002 PHE R 338 TRP 0.008 0.001 TRP R 436 HIS 0.003 0.001 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5618) covalent geometry : angle 0.54035 ( 7616) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.49789 ( 16) hydrogen bonds : bond 0.02920 ( 190) hydrogen bonds : angle 6.13709 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.5971 (mmm) cc_final: 0.5703 (mmm) REVERT: D 29 PHE cc_start: 0.6471 (OUTLIER) cc_final: 0.6235 (t80) outliers start: 17 outliers final: 15 residues processed: 87 average time/residue: 0.2156 time to fit residues: 22.8549 Evaluate side-chains 92 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.107762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.095286 restraints weight = 89879.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.098091 restraints weight = 45452.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.099789 restraints weight = 28562.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.100854 restraints weight = 20811.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.101524 restraints weight = 16772.977| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 5626 Z= 0.188 Angle : 0.591 5.859 7632 Z= 0.325 Chirality : 0.043 0.194 793 Planarity : 0.006 0.119 996 Dihedral : 5.700 34.388 789 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.13 % Favored : 89.15 % Rotamer: Outliers : 3.63 % Allowed : 13.30 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.69 (0.32), residues: 691 helix: -4.66 (0.82), residues: 8 sheet: -0.23 (0.33), residues: 251 loop : -1.68 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.014 0.002 TYR R 365 PHE 0.023 0.002 PHE R 338 TRP 0.012 0.001 TRP R 436 HIS 0.006 0.002 HIS R 519 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 5618) covalent geometry : angle 0.59066 ( 7616) SS BOND : bond 0.00287 ( 8) SS BOND : angle 0.62308 ( 16) hydrogen bonds : bond 0.03415 ( 190) hydrogen bonds : angle 6.28542 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6614 (m100) cc_final: 0.5933 (m100) REVERT: D 29 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6593 (t80) REVERT: R 433 VAL cc_start: 0.4948 (OUTLIER) cc_final: 0.4521 (p) outliers start: 21 outliers final: 17 residues processed: 85 average time/residue: 0.1990 time to fit residues: 20.8094 Evaluate side-chains 90 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.107268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.094835 restraints weight = 90664.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.097659 restraints weight = 45392.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.099358 restraints weight = 28372.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.100409 restraints weight = 20634.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.101045 restraints weight = 16619.973| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 5626 Z= 0.177 Angle : 0.586 5.728 7632 Z= 0.320 Chirality : 0.043 0.189 793 Planarity : 0.005 0.118 996 Dihedral : 5.746 33.011 789 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.13 % Favored : 89.15 % Rotamer: Outliers : 3.45 % Allowed : 13.47 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.77 (0.32), residues: 691 helix: -4.60 (0.88), residues: 8 sheet: -0.30 (0.33), residues: 251 loop : -1.73 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 113 TYR 0.014 0.002 TYR B 112 PHE 0.024 0.002 PHE R 338 TRP 0.011 0.001 TRP R 436 HIS 0.004 0.002 HIS R 519 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5618) covalent geometry : angle 0.58553 ( 7616) SS BOND : bond 0.00240 ( 8) SS BOND : angle 0.71717 ( 16) hydrogen bonds : bond 0.03379 ( 190) hydrogen bonds : angle 6.28710 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.6076 (mmm) cc_final: 0.5233 (mmm) REVERT: C 104 GLU cc_start: 0.6175 (mp0) cc_final: 0.5949 (mp0) REVERT: D 29 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6808 (t80) outliers start: 20 outliers final: 17 residues processed: 84 average time/residue: 0.2040 time to fit residues: 21.3614 Evaluate side-chains 87 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.107168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.093509 restraints weight = 77851.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.096874 restraints weight = 37277.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.098842 restraints weight = 22139.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.100053 restraints weight = 15445.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.100754 restraints weight = 12096.378| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 5626 Z= 0.162 Angle : 0.583 5.627 7632 Z= 0.317 Chirality : 0.043 0.189 793 Planarity : 0.005 0.118 996 Dihedral : 5.730 35.052 789 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.00 % Favored : 88.28 % Rotamer: Outliers : 3.45 % Allowed : 13.64 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.32), residues: 691 helix: -4.52 (0.95), residues: 8 sheet: -0.18 (0.34), residues: 244 loop : -1.74 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 53 TYR 0.013 0.002 TYR D 114 PHE 0.024 0.002 PHE R 338 TRP 0.011 0.001 TRP R 436 HIS 0.004 0.002 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5618) covalent geometry : angle 0.58281 ( 7616) SS BOND : bond 0.00210 ( 8) SS BOND : angle 0.83944 ( 16) hydrogen bonds : bond 0.03220 ( 190) hydrogen bonds : angle 6.29745 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6741 (t80) outliers start: 20 outliers final: 19 residues processed: 79 average time/residue: 0.1872 time to fit residues: 18.3815 Evaluate side-chains 87 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 53 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.107986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.094374 restraints weight = 77680.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.097768 restraints weight = 37186.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.099737 restraints weight = 21993.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.100932 restraints weight = 15279.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.101727 restraints weight = 11938.661| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 5626 Z= 0.137 Angle : 0.560 5.593 7632 Z= 0.303 Chirality : 0.043 0.182 793 Planarity : 0.005 0.117 996 Dihedral : 5.530 33.177 789 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.26 % Favored : 90.01 % Rotamer: Outliers : 3.28 % Allowed : 13.82 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.74 (0.32), residues: 691 helix: -4.15 (1.31), residues: 8 sheet: -0.22 (0.33), residues: 248 loop : -1.74 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.012 0.001 TYR D 114 PHE 0.022 0.002 PHE R 338 TRP 0.010 0.001 TRP R 436 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5618) covalent geometry : angle 0.55976 ( 7616) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.73193 ( 16) hydrogen bonds : bond 0.02998 ( 190) hydrogen bonds : angle 6.11385 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 31 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue ILE 87 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue ILE 358 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 418 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 468 is missing expected H atoms. Skipping. Residue ILE 472 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6581 (m100) cc_final: 0.6128 (m100) REVERT: C 79 LEU cc_start: 0.9216 (tp) cc_final: 0.8932 (tp) REVERT: D 29 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6827 (t80) outliers start: 19 outliers final: 18 residues processed: 80 average time/residue: 0.1829 time to fit residues: 18.3195 Evaluate side-chains 86 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.108890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.096541 restraints weight = 90649.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.099352 restraints weight = 44991.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.101103 restraints weight = 28050.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.102143 restraints weight = 20243.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.102799 restraints weight = 16252.459| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 5626 Z= 0.115 Angle : 0.554 5.648 7632 Z= 0.297 Chirality : 0.043 0.179 793 Planarity : 0.005 0.116 996 Dihedral : 5.378 30.401 789 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.84 % Favored : 89.44 % Rotamer: Outliers : 2.94 % Allowed : 15.03 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.68 (0.32), residues: 691 helix: -3.92 (1.53), residues: 8 sheet: -0.17 (0.34), residues: 246 loop : -1.71 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.011 0.001 TYR D 114 PHE 0.021 0.002 PHE R 338 TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5618) covalent geometry : angle 0.55371 ( 7616) SS BOND : bond 0.00168 ( 8) SS BOND : angle 0.70090 ( 16) hydrogen bonds : bond 0.02840 ( 190) hydrogen bonds : angle 6.02689 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.79 seconds wall clock time: 43 minutes 43.48 seconds (2623.48 seconds total)