Starting phenix.real_space_refine on Mon Jul 28 19:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyj_27080/07_2025/8cyj_27080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyj_27080/07_2025/8cyj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cyj_27080/07_2025/8cyj_27080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyj_27080/07_2025/8cyj_27080.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyj_27080/07_2025/8cyj_27080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyj_27080/07_2025/8cyj_27080.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.29, per 1000 atoms: 0.50 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: 2.69 Conformation dependent library (CDL) restraints added in 700.8 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: 0.99 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: 3.59 Time building geometry restraints manager: 3.26 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: 18.220 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: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.260 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.110 ------------------------------------------------------------------------------- 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 : 7.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.001 TRP A 53 HIS 0.001 0.000 HIS D 113 PHE 0.009 0.001 PHE B 29 TYR 0.006 0.001 TYR D 114 ARG 0.014 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.14285 ( 190) hydrogen bonds : angle 7.37863 ( 474) SS BOND : bond 0.00199 ( 8) SS BOND : angle 0.49491 ( 16) covalent geometry : bond 0.00267 ( 5618) covalent geometry : angle 0.61883 ( 7616) *********************** 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 : 0.832 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: 0.5005 time to fit residues: 56.9666 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 : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.114549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.102187 restraints weight = 89978.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.105112 restraints weight = 45650.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.106861 restraints weight = 28373.154| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 5626 Z= 0.222 Angle : 0.667 7.012 7632 Z= 0.367 Chirality : 0.045 0.197 793 Planarity : 0.007 0.128 996 Dihedral : 5.859 33.469 789 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 1.01 % Allowed : 7.24 % Favored : 91.75 % Rotamer: Outliers : 1.73 % Allowed : 6.56 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.31), residues: 691 helix: -4.57 (0.93), residues: 8 sheet: 0.08 (0.32), residues: 249 loop : -1.41 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 53 HIS 0.003 0.002 HIS B 59 PHE 0.019 0.002 PHE R 377 TYR 0.020 0.002 TYR C 106 ARG 0.007 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 190) hydrogen bonds : angle 6.50143 ( 474) SS BOND : bond 0.00314 ( 8) SS BOND : angle 1.39286 ( 16) covalent geometry : bond 0.00477 ( 5618) covalent geometry : angle 0.66432 ( 7616) *********************** 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 92 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.772 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: C 36 TRP cc_start: 0.5713 (m100) cc_final: 0.4706 (m100) REVERT: D 44 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7988 (tm-30) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.6115 time to fit residues: 64.7718 Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR 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 69 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 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 82 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.110815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.098404 restraints weight = 91082.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.101321 restraints weight = 46128.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.103099 restraints weight = 28649.767| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5626 Z= 0.221 Angle : 0.640 6.956 7632 Z= 0.352 Chirality : 0.044 0.195 793 Planarity : 0.006 0.127 996 Dihedral : 6.069 35.959 789 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.54 % Favored : 90.59 % Rotamer: Outliers : 3.11 % Allowed : 9.33 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.32), residues: 691 helix: -4.67 (0.83), residues: 8 sheet: 0.02 (0.33), residues: 249 loop : -1.65 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 436 HIS 0.007 0.003 HIS R 519 PHE 0.019 0.003 PHE R 392 TYR 0.024 0.002 TYR C 106 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 190) hydrogen bonds : angle 6.61686 ( 474) SS BOND : bond 0.00313 ( 8) SS BOND : angle 1.20807 ( 16) covalent geometry : bond 0.00473 ( 5618) covalent geometry : angle 0.63795 ( 7616) *********************** 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 92 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.862 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: A 52 ARG cc_start: 0.6561 (ttm110) cc_final: 0.6051 (ttp-110) REVERT: C 104 GLU cc_start: 0.5135 (tt0) cc_final: 0.3503 (mp0) REVERT: D 44 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8006 (tm-30) REVERT: R 383 SER cc_start: 0.4212 (OUTLIER) cc_final: 0.3678 (t) outliers start: 18 outliers final: 16 residues processed: 86 average time/residue: 0.5113 time to fit residues: 53.4258 Evaluate side-chains 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 81 LEU 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 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 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4567 r_free = 0.4567 target = 0.106294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.092089 restraints weight = 79506.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.095394 restraints weight = 40685.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.097439 restraints weight = 25082.366| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 5626 Z= 0.255 Angle : 0.672 6.555 7632 Z= 0.373 Chirality : 0.045 0.203 793 Planarity : 0.006 0.125 996 Dihedral : 6.375 44.170 789 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.56 % Favored : 88.57 % Rotamer: Outliers : 3.63 % Allowed : 12.09 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.31), residues: 691 helix: -4.97 (0.56), residues: 8 sheet: -0.14 (0.33), residues: 236 loop : -1.84 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 436 HIS 0.007 0.003 HIS R 519 PHE 0.020 0.003 PHE R 338 TYR 0.022 0.002 TYR C 106 ARG 0.004 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 190) hydrogen bonds : angle 6.75822 ( 474) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.91339 ( 16) covalent geometry : bond 0.00542 ( 5618) covalent geometry : angle 0.67143 ( 7616) *********************** 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 95 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.014 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: A 25 SER cc_start: 0.8973 (m) cc_final: 0.8715 (t) REVERT: D 29 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6352 (t80) REVERT: R 433 VAL cc_start: 0.5360 (OUTLIER) cc_final: 0.4911 (p) outliers start: 21 outliers final: 17 residues processed: 86 average time/residue: 0.4902 time to fit residues: 51.6440 Evaluate side-chains 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.108116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.095723 restraints weight = 89954.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.098588 restraints weight = 45090.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.100268 restraints weight = 28161.746| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 5626 Z= 0.151 Angle : 0.591 6.506 7632 Z= 0.320 Chirality : 0.044 0.190 793 Planarity : 0.005 0.124 996 Dihedral : 5.929 41.759 789 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.12 % Favored : 90.01 % Rotamer: Outliers : 2.76 % Allowed : 13.64 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.32), residues: 691 helix: -4.85 (0.66), residues: 8 sheet: -0.30 (0.33), residues: 256 loop : -1.85 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.005 0.002 HIS C 103 PHE 0.022 0.002 PHE R 338 TYR 0.014 0.001 TYR C 106 ARG 0.002 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 190) hydrogen bonds : angle 6.48389 ( 474) SS BOND : bond 0.00245 ( 8) SS BOND : angle 1.65474 ( 16) covalent geometry : bond 0.00338 ( 5618) covalent geometry : angle 0.58674 ( 7616) *********************** 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 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.817 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: C 79 LEU cc_start: 0.9338 (tp) cc_final: 0.9115 (tp) REVERT: C 83 MET cc_start: 0.8000 (mtm) cc_final: 0.7733 (ptp) REVERT: D 29 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6680 (t80) REVERT: R 433 VAL cc_start: 0.5199 (OUTLIER) cc_final: 0.4757 (p) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.4509 time to fit residues: 44.7521 Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 124 VAL 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 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 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.107716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.095293 restraints weight = 90686.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.098112 restraints weight = 45570.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.099808 restraints weight = 28563.410| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 5626 Z= 0.148 Angle : 0.588 6.397 7632 Z= 0.318 Chirality : 0.043 0.191 793 Planarity : 0.005 0.123 996 Dihedral : 5.733 34.239 789 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.84 % Favored : 89.44 % Rotamer: Outliers : 3.80 % Allowed : 13.82 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.32), residues: 691 helix: -4.81 (0.68), residues: 8 sheet: -0.33 (0.33), residues: 254 loop : -1.78 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.004 0.001 HIS B 59 PHE 0.023 0.002 PHE R 338 TYR 0.012 0.002 TYR D 114 ARG 0.002 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 190) hydrogen bonds : angle 6.35670 ( 474) SS BOND : bond 0.00230 ( 8) SS BOND : angle 1.47077 ( 16) covalent geometry : bond 0.00333 ( 5618) covalent geometry : angle 0.58433 ( 7616) *********************** 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 90 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.930 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: B 34 MET cc_start: 0.1828 (mmt) cc_final: 0.1117 (mmm) REVERT: C 36 TRP cc_start: 0.6574 (m100) cc_final: 0.6157 (m100) REVERT: C 79 LEU cc_start: 0.9332 (tp) cc_final: 0.9052 (tp) REVERT: D 29 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6633 (t80) REVERT: R 383 SER cc_start: 0.3958 (OUTLIER) cc_final: 0.3357 (t) outliers start: 22 outliers final: 18 residues processed: 82 average time/residue: 0.4543 time to fit residues: 46.8824 Evaluate side-chains 85 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 124 VAL 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 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.4598 r_free = 0.4598 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.096283 restraints weight = 90680.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.099148 restraints weight = 45630.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.100844 restraints weight = 28497.620| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 5626 Z= 0.120 Angle : 0.560 6.129 7632 Z= 0.301 Chirality : 0.043 0.185 793 Planarity : 0.005 0.121 996 Dihedral : 5.552 35.568 789 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.26 % Favored : 90.01 % Rotamer: Outliers : 2.94 % Allowed : 15.37 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.32), residues: 691 helix: -4.73 (0.75), residues: 8 sheet: -0.32 (0.33), residues: 255 loop : -1.71 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS C 103 PHE 0.024 0.002 PHE R 338 TYR 0.011 0.001 TYR D 114 ARG 0.001 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 190) hydrogen bonds : angle 6.20991 ( 474) SS BOND : bond 0.00180 ( 8) SS BOND : angle 1.30786 ( 16) covalent geometry : bond 0.00284 ( 5618) covalent geometry : angle 0.55716 ( 7616) *********************** 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 85 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.895 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: B 34 MET cc_start: 0.1587 (mmt) cc_final: 0.1036 (mmm) REVERT: C 36 TRP cc_start: 0.6744 (m100) cc_final: 0.6236 (m100) REVERT: C 79 LEU cc_start: 0.9325 (tp) cc_final: 0.9061 (tp) REVERT: D 29 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6671 (t80) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.4541 time to fit residues: 44.9512 Evaluate side-chains 82 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 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 = 0.4584 r_free = 0.4584 target = 0.107751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.095464 restraints weight = 89400.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.098248 restraints weight = 44947.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.099900 restraints weight = 28081.600| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.4964 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= 0.139 Angle : 0.570 5.915 7632 Z= 0.310 Chirality : 0.043 0.188 793 Planarity : 0.005 0.119 996 Dihedral : 5.519 34.001 789 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.56 % Favored : 88.71 % Rotamer: Outliers : 3.63 % Allowed : 14.85 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.32), residues: 691 helix: -4.54 (0.92), residues: 8 sheet: -0.37 (0.33), residues: 255 loop : -1.70 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.004 0.002 HIS B 59 PHE 0.029 0.002 PHE R 338 TYR 0.012 0.001 TYR D 114 ARG 0.002 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 190) hydrogen bonds : angle 6.19332 ( 474) SS BOND : bond 0.00192 ( 8) SS BOND : angle 1.07887 ( 16) covalent geometry : bond 0.00319 ( 5618) covalent geometry : angle 0.56854 ( 7616) *********************** 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 86 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.844 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: C 36 TRP cc_start: 0.6522 (m100) cc_final: 0.6196 (m100) REVERT: C 79 LEU cc_start: 0.9313 (tp) cc_final: 0.9044 (tp) REVERT: C 83 MET cc_start: 0.8108 (mtm) cc_final: 0.7748 (ptp) REVERT: D 29 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6744 (t80) REVERT: R 383 SER cc_start: 0.4328 (OUTLIER) cc_final: 0.3901 (t) outliers start: 21 outliers final: 19 residues processed: 78 average time/residue: 0.4517 time to fit residues: 44.2460 Evaluate side-chains 83 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 29 PHE 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 95 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 124 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 519 HIS ** 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 = 0.4529 r_free = 0.4529 target = 0.104591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.092453 restraints weight = 92818.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.095199 restraints weight = 47334.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.096816 restraints weight = 29674.364| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 5626 Z= 0.228 Angle : 0.658 5.751 7632 Z= 0.363 Chirality : 0.045 0.195 793 Planarity : 0.006 0.118 996 Dihedral : 6.063 37.866 789 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.29 % Favored : 87.99 % Rotamer: Outliers : 4.49 % Allowed : 14.68 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.56 (0.34), residues: 246 loop : -1.87 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 436 HIS 0.007 0.003 HIS B 59 PHE 0.027 0.003 PHE R 338 TYR 0.020 0.002 TYR C 106 ARG 0.003 0.001 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 190) hydrogen bonds : angle 6.70338 ( 474) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.83099 ( 16) covalent geometry : bond 0.00495 ( 5618) covalent geometry : angle 0.65729 ( 7616) *********************** 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 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.933 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 79 LEU cc_start: 0.9410 (tp) cc_final: 0.9007 (tt) outliers start: 26 outliers final: 23 residues processed: 80 average time/residue: 0.4100 time to fit residues: 41.9001 Evaluate side-chains 85 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 29 PHE 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 83 MET Chi-restraints excluded: chain B residue 95 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 124 VAL 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 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 32 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.106470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.094176 restraints weight = 90357.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.096970 restraints weight = 45142.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.098608 restraints weight = 28107.419| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.5652 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= 0.158 Angle : 0.603 5.995 7632 Z= 0.329 Chirality : 0.044 0.189 793 Planarity : 0.006 0.117 996 Dihedral : 5.814 34.456 789 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.56 % Favored : 88.57 % Rotamer: Outliers : 3.28 % Allowed : 16.41 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.56 (0.34), residues: 246 loop : -1.85 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 36 HIS 0.004 0.002 HIS C 103 PHE 0.026 0.002 PHE R 338 TYR 0.014 0.001 TYR D 114 ARG 0.010 0.001 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 190) hydrogen bonds : angle 6.51698 ( 474) SS BOND : bond 0.00225 ( 8) SS BOND : angle 0.66036 ( 16) covalent geometry : bond 0.00356 ( 5618) covalent geometry : angle 0.60272 ( 7616) ********************** 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 84 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.846 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: C 79 LEU cc_start: 0.9370 (tp) cc_final: 0.9026 (tp) outliers start: 19 outliers final: 17 residues processed: 78 average time/residue: 0.4391 time to fit residues: 43.7660 Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 95 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 D residue 69 THR 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 42 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 519 HIS ** 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 = 0.4549 r_free = 0.4549 target = 0.105685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.093379 restraints weight = 90553.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.096174 restraints weight = 45317.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.097824 restraints weight = 28232.257| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 5626 Z= 0.166 Angle : 0.615 5.977 7632 Z= 0.334 Chirality : 0.044 0.189 793 Planarity : 0.006 0.116 996 Dihedral : 5.846 35.780 789 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.29 % Favored : 87.84 % Rotamer: Outliers : 3.28 % Allowed : 16.58 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.54 (0.34), residues: 246 loop : -1.88 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.004 0.002 HIS B 59 PHE 0.043 0.002 PHE D 29 TYR 0.016 0.002 TYR D 114 ARG 0.006 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 190) hydrogen bonds : angle 6.59483 ( 474) SS BOND : bond 0.00246 ( 8) SS BOND : angle 1.31954 ( 16) covalent geometry : bond 0.00373 ( 5618) covalent geometry : angle 0.61255 ( 7616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5037.69 seconds wall clock time: 86 minutes 41.22 seconds (5201.22 seconds total)