Starting phenix.real_space_refine on Sun Dec 29 13:26:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyj_27080/12_2024/8cyj_27080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyj_27080/12_2024/8cyj_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_27080/12_2024/8cyj_27080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyj_27080/12_2024/8cyj_27080.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyj_27080/12_2024/8cyj_27080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyj_27080/12_2024/8cyj_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-5532/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: 5.72, per 1000 atoms: 0.54 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: 3.39 Conformation dependent library (CDL) restraints added in 841.8 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: 1.12 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: 3.98 Time building geometry restraints manager: 3.63 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: 0.750 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.080 Find NCS groups from input model: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- 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 5618 Z= 0.180 Angle : 0.619 6.883 7616 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 *********************** 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 : 0.900 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: 0.5126 time to fit residues: 57.8338 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 : 0.958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 5618 Z= 0.317 Angle : 0.664 6.989 7616 Z= 0.366 Chirality : 0.045 0.197 793 Planarity : 0.007 0.128 996 Dihedral : 5.858 33.476 789 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 1.01 % Allowed : 7.24 % Favored : 91.75 % Rotamer: Outliers : 1.90 % Allowed : 6.39 % 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 *********************** 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 93 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.947 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: 0.5883 (m100) cc_final: 0.4807 (m100) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 0.6192 time to fit residues: 65.5216 Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 C residue 83 MET 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 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 5618 Z= 0.229 Angle : 0.573 6.760 7616 Z= 0.312 Chirality : 0.043 0.187 793 Planarity : 0.006 0.126 996 Dihedral : 5.611 34.403 789 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.53 % Favored : 91.61 % Rotamer: Outliers : 2.07 % Allowed : 9.67 % Favored : 88.26 % 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: -1.30 (0.32), residues: 691 helix: -4.26 (1.22), residues: 8 sheet: 0.08 (0.32), residues: 249 loop : -1.43 (0.30), residues: 434 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 0.018 0.002 PHE R 338 TYR 0.014 0.002 TYR C 106 ARG 0.003 0.001 ARG A 75 *********************** 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 85 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.823 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 36 TRP cc_start: 0.6281 (m100) cc_final: 0.5419 (m100) REVERT: C 104 GLU cc_start: 0.5308 (tt0) cc_final: 0.3938 (mp0) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.5397 time to fit residues: 52.1194 Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 5618 Z= 0.200 Angle : 0.549 6.478 7616 Z= 0.296 Chirality : 0.043 0.187 793 Planarity : 0.005 0.124 996 Dihedral : 5.431 38.853 789 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.81 % Favored : 91.46 % Rotamer: Outliers : 2.59 % Allowed : 11.23 % Favored : 86.18 % 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: -1.35 (0.32), residues: 691 helix: -4.31 (1.17), residues: 8 sheet: 0.08 (0.32), residues: 259 loop : -1.52 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.003 0.001 HIS B 59 PHE 0.022 0.002 PHE R 338 TYR 0.014 0.001 TYR C 52 ARG 0.003 0.000 ARG A 75 *********************** 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 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.909 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: C 36 TRP cc_start: 0.6486 (m100) cc_final: 0.5502 (m100) REVERT: D 29 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.6442 (t80) outliers start: 15 outliers final: 13 residues processed: 82 average time/residue: 0.5335 time to fit residues: 53.1460 Evaluate side-chains 86 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 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 402 ILE Chi-restraints excluded: chain R residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 5618 Z= 0.432 Angle : 0.745 6.318 7616 Z= 0.412 Chirality : 0.046 0.207 793 Planarity : 0.006 0.122 996 Dihedral : 6.435 41.742 789 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.42 % Favored : 88.71 % Rotamer: Outliers : 3.80 % Allowed : 12.09 % Favored : 84.11 % 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: -1.93 (0.31), residues: 691 helix: -4.87 (0.65), residues: 8 sheet: -0.29 (0.33), residues: 241 loop : -1.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 106 HIS 0.011 0.004 HIS R 519 PHE 0.025 0.003 PHE R 392 TYR 0.031 0.003 TYR C 106 ARG 0.004 0.001 ARG B 72 *********************** 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 94 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.981 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: C 36 TRP cc_start: 0.6239 (m100) cc_final: 0.5844 (m100) REVERT: C 79 LEU cc_start: 0.9083 (tp) cc_final: 0.8817 (tp) REVERT: D 29 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6485 (t80) REVERT: R 433 VAL cc_start: 0.5716 (OUTLIER) cc_final: 0.5233 (p) outliers start: 22 outliers final: 17 residues processed: 85 average time/residue: 0.4473 time to fit residues: 47.8268 Evaluate side-chains 86 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 5618 Z= 0.260 Angle : 0.604 6.413 7616 Z= 0.330 Chirality : 0.044 0.191 793 Planarity : 0.006 0.122 996 Dihedral : 5.994 39.183 789 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.41 % Favored : 89.73 % Rotamer: Outliers : 4.15 % Allowed : 12.44 % Favored : 83.42 % 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: -1.89 (0.32), residues: 691 helix: -4.83 (0.66), residues: 8 sheet: -0.27 (0.33), residues: 251 loop : -1.88 (0.30), residues: 432 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 0.023 0.002 PHE R 338 TYR 0.017 0.002 TYR C 106 ARG 0.005 0.001 ARG A 52 *********************** 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 98 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.944 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 36 TRP cc_start: 0.6371 (m100) cc_final: 0.5896 (m100) REVERT: C 79 LEU cc_start: 0.9007 (tp) cc_final: 0.8777 (tp) REVERT: D 29 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6503 (t80) REVERT: R 383 SER cc_start: 0.4323 (OUTLIER) cc_final: 0.3893 (t) outliers start: 24 outliers final: 18 residues processed: 88 average time/residue: 0.4419 time to fit residues: 49.1413 Evaluate side-chains 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 11 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 5618 Z= 0.251 Angle : 0.605 6.417 7616 Z= 0.329 Chirality : 0.044 0.192 793 Planarity : 0.006 0.121 996 Dihedral : 5.889 37.111 789 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.42 % Favored : 88.86 % Rotamer: Outliers : 3.80 % Allowed : 14.34 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (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: -1.95 (0.32), residues: 691 helix: -4.83 (0.65), residues: 8 sheet: -0.34 (0.33), residues: 251 loop : -1.91 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 436 HIS 0.004 0.002 HIS B 59 PHE 0.012 0.002 PHE R 429 TYR 0.017 0.002 TYR C 106 ARG 0.005 0.001 ARG A 52 *********************** 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 91 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.047 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: B 86 LEU cc_start: 0.3741 (mp) cc_final: 0.3474 (mt) REVERT: C 36 TRP cc_start: 0.6228 (m100) cc_final: 0.5904 (m100) REVERT: C 79 LEU cc_start: 0.9039 (tp) cc_final: 0.8836 (tp) outliers start: 22 outliers final: 21 residues processed: 82 average time/residue: 0.5147 time to fit residues: 51.8427 Evaluate side-chains 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 5618 Z= 0.216 Angle : 0.571 6.069 7616 Z= 0.310 Chirality : 0.043 0.186 793 Planarity : 0.005 0.120 996 Dihedral : 5.714 35.181 789 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.13 % Favored : 89.15 % Rotamer: Outliers : 3.11 % Allowed : 14.68 % Favored : 82.21 % 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: -1.95 (0.32), residues: 691 helix: -4.33 (1.12), residues: 8 sheet: -0.47 (0.33), residues: 255 loop : -1.84 (0.30), residues: 428 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 0.010 0.002 PHE R 429 TYR 0.012 0.001 TYR D 114 ARG 0.005 0.000 ARG A 52 *********************** 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: 18 poor density : 68 time to evaluate : 0.905 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 36 TRP cc_start: 0.6363 (m100) cc_final: 0.5932 (m100) REVERT: C 79 LEU cc_start: 0.9015 (tp) cc_final: 0.8789 (tp) REVERT: C 83 MET cc_start: 0.6766 (ptp) cc_final: 0.6560 (ptp) REVERT: D 29 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6904 (t80) outliers start: 18 outliers final: 17 residues processed: 78 average time/residue: 0.4978 time to fit residues: 47.7239 Evaluate side-chains 84 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 5618 Z= 0.292 Angle : 0.630 6.283 7616 Z= 0.346 Chirality : 0.044 0.193 793 Planarity : 0.006 0.119 996 Dihedral : 5.998 35.943 789 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.16 % Favored : 87.12 % Rotamer: Outliers : 3.63 % Allowed : 14.68 % 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: -1.98 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.39 (0.34), residues: 243 loop : -1.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 436 HIS 0.006 0.002 HIS B 59 PHE 0.015 0.002 PHE R 392 TYR 0.017 0.002 TYR B 112 ARG 0.005 0.001 ARG D 72 *********************** 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 86 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.885 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 36 TRP cc_start: 0.6262 (m100) cc_final: 0.6040 (m100) REVERT: C 79 LEU cc_start: 0.9059 (tp) cc_final: 0.8822 (tp) outliers start: 21 outliers final: 20 residues processed: 76 average time/residue: 0.4443 time to fit residues: 42.8290 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 : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 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 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 124 VAL 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 403 ARG 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 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 5618 Z= 0.201 Angle : 0.571 5.836 7616 Z= 0.309 Chirality : 0.043 0.183 793 Planarity : 0.005 0.118 996 Dihedral : 5.664 33.669 789 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.97 % Favored : 90.30 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (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: -1.88 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.41 (0.33), residues: 246 loop : -1.84 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.003 0.001 HIS B 59 PHE 0.043 0.002 PHE D 29 TYR 0.013 0.001 TYR D 114 ARG 0.005 0.000 ARG A 52 ********************** 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 82 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.955 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: C 36 TRP cc_start: 0.6324 (m100) cc_final: 0.5884 (m100) outliers start: 15 outliers final: 15 residues processed: 74 average time/residue: 0.4587 time to fit residues: 42.6773 Evaluate side-chains 78 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 95 TYR 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 403 ARG 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 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.106545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.094206 restraints weight = 91534.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.097000 restraints weight = 46268.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.098612 restraints weight = 28968.768| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 5618 Z= 0.238 Angle : 0.597 6.131 7616 Z= 0.325 Chirality : 0.044 0.187 793 Planarity : 0.005 0.117 996 Dihedral : 5.693 33.870 789 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.43 % Favored : 87.84 % Rotamer: Outliers : 2.94 % Allowed : 15.89 % Favored : 81.17 % 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: -1.96 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.46 (0.33), residues: 243 loop : -1.89 (0.29), residues: 448 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 0.032 0.002 PHE D 29 TYR 0.013 0.001 TYR D 114 ARG 0.004 0.001 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.04 seconds wall clock time: 61 minutes 18.82 seconds (3678.82 seconds total)