Starting phenix.real_space_refine on Fri Feb 14 20:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyj_27080/02_2025/8cyj_27080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyj_27080/02_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_27080/02_2025/8cyj_27080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyj_27080/02_2025/8cyj_27080.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyj_27080/02_2025/8cyj_27080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyj_27080/02_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-5592/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: 5.06, per 1000 atoms: 0.48 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: 2.83 Conformation dependent library (CDL) restraints added in 771.2 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: 1.27 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: 3.90 Time building geometry restraints manager: 3.33 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: 0.880 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: 0.090 Set scattering table: 0.120 Process input model: 25.620 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- 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 : 0.940 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: 0.5134 time to fit residues: 58.3050 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 : 0.790 ------------------------------------------------------------------------------- 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 = 0.114560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.102198 restraints weight = 89980.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.105112 restraints weight = 45557.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.106858 restraints weight = 28401.505| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 : 0.896 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: 0.5763 (m100) cc_final: 0.4736 (m100) REVERT: D 44 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7974 (tm-30) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 0.6105 time to fit residues: 64.6084 Evaluate side-chains 82 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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: 0.0050 chunk 0 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 = 0.4636 r_free = 0.4636 target = 0.110739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.098321 restraints weight = 91054.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.101245 restraints weight = 46192.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.103024 restraints weight = 28659.751| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5618 Z= 0.312 Angle : 0.645 6.951 7616 Z= 0.355 Chirality : 0.044 0.197 793 Planarity : 0.006 0.126 996 Dihedral : 6.067 35.915 789 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.83 % Favored : 90.30 % 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: -1.51 (0.32), residues: 691 helix: -4.62 (0.89), residues: 8 sheet: 0.07 (0.33), residues: 246 loop : -1.66 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 436 HIS 0.007 0.003 HIS R 519 PHE 0.020 0.003 PHE R 392 TYR 0.025 0.002 TYR C 106 ARG 0.007 0.001 ARG R 357 *********************** 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 91 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.882 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: 0.6565 (ttm110) cc_final: 0.6054 (ttp-110) REVERT: C 104 GLU cc_start: 0.5256 (tt0) cc_final: 0.3756 (mp0) REVERT: D 44 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8022 (tm-30) outliers start: 18 outliers final: 16 residues processed: 84 average time/residue: 0.5388 time to fit residues: 54.6967 Evaluate side-chains 86 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.106829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.094340 restraints weight = 90846.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.097126 restraints weight = 47017.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.098848 restraints weight = 29698.098| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4376 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= 0.323 Angle : 0.654 6.553 7616 Z= 0.362 Chirality : 0.045 0.202 793 Planarity : 0.006 0.125 996 Dihedral : 6.277 42.637 789 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.42 % Favored : 88.71 % Rotamer: Outliers : 4.15 % Allowed : 11.74 % 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: -1.86 (0.31), residues: 691 helix: -4.90 (0.61), residues: 8 sheet: -0.24 (0.33), residues: 241 loop : -1.84 (0.29), residues: 442 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 0.021 0.003 PHE R 338 TYR 0.020 0.002 TYR R 365 ARG 0.005 0.001 ARG R 357 *********************** 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 99 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.840 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 25 SER cc_start: 0.9060 (m) cc_final: 0.8798 (t) REVERT: C 34 MET cc_start: 0.5823 (mmm) cc_final: 0.5429 (mmm) REVERT: D 29 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6357 (t80) REVERT: R 417 LYS cc_start: 0.8850 (mttt) cc_final: 0.8646 (mmmm) outliers start: 24 outliers final: 19 residues processed: 90 average time/residue: 0.5290 time to fit residues: 59.1153 Evaluate side-chains 91 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.108122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.095638 restraints weight = 90133.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.098497 restraints weight = 45662.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.100255 restraints weight = 28547.694| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.4439 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= 0.221 Angle : 0.584 6.543 7616 Z= 0.317 Chirality : 0.044 0.189 793 Planarity : 0.005 0.124 996 Dihedral : 5.848 41.693 789 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.97 % Favored : 90.16 % Rotamer: Outliers : 3.11 % Allowed : 12.95 % Favored : 83.94 % 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: -1.85 (0.32), residues: 691 helix: -4.84 (0.66), residues: 8 sheet: -0.31 (0.33), residues: 258 loop : -1.82 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 HIS 0.004 0.002 HIS B 59 PHE 0.010 0.002 PHE R 429 TYR 0.015 0.001 TYR C 106 ARG 0.002 0.000 ARG D 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: 18 poor density : 76 time to evaluate : 0.865 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: 0.1371 (mmt) cc_final: 0.0627 (mmm) REVERT: C 34 MET cc_start: 0.5587 (mmm) cc_final: 0.5353 (mmm) REVERT: C 36 TRP cc_start: 0.6822 (m100) cc_final: 0.6007 (m100) REVERT: C 83 MET cc_start: 0.8151 (mtm) cc_final: 0.7872 (ptp) REVERT: D 29 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6669 (t80) REVERT: R 417 LYS cc_start: 0.8822 (mttt) cc_final: 0.8619 (mmmm) outliers start: 18 outliers final: 16 residues processed: 86 average time/residue: 0.5276 time to fit residues: 55.3869 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 : 0.814 ------------------------------------------------------------------------------- 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 104 GLU 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: 1.9990 chunk 28 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4600 r_free = 0.4600 target = 0.108888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.096419 restraints weight = 90412.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.099316 restraints weight = 45560.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.101056 restraints weight = 28389.946| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4632 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= 0.204 Angle : 0.565 6.577 7616 Z= 0.306 Chirality : 0.043 0.188 793 Planarity : 0.005 0.122 996 Dihedral : 5.664 37.480 789 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.84 % Favored : 89.44 % Rotamer: Outliers : 3.63 % Allowed : 13.64 % Favored : 82.73 % 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: -1.78 (0.32), residues: 691 helix: -4.75 (0.73), residues: 8 sheet: -0.25 (0.33), residues: 256 loop : -1.78 (0.30), residues: 427 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 0.010 0.002 PHE R 486 TYR 0.012 0.001 TYR D 114 ARG 0.004 0.000 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 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 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: B 34 MET cc_start: 0.1719 (mmt) cc_final: 0.1119 (mmm) REVERT: C 36 TRP cc_start: 0.6802 (m100) cc_final: 0.5953 (m100) REVERT: D 29 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6613 (t80) REVERT: D 38 ARG cc_start: 0.8312 (ptt-90) cc_final: 0.8052 (ptt-90) REVERT: R 383 SER cc_start: 0.4339 (OUTLIER) cc_final: 0.3942 (t) outliers start: 21 outliers final: 18 residues processed: 82 average time/residue: 0.4513 time to fit residues: 46.1752 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 : 0.921 ------------------------------------------------------------------------------- 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 81 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 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=2.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.104730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.091130 restraints weight = 79453.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.094248 restraints weight = 40115.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.096079 restraints weight = 24750.777| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.5212 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= 0.274 Angle : 0.611 6.402 7616 Z= 0.335 Chirality : 0.044 0.194 793 Planarity : 0.005 0.120 996 Dihedral : 5.916 38.655 789 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.43 % Favored : 87.84 % Rotamer: Outliers : 4.32 % Allowed : 13.30 % 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: -1.91 (0.32), residues: 691 helix: -4.88 (0.62), residues: 8 sheet: -0.40 (0.33), residues: 252 loop : -1.81 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 436 HIS 0.005 0.002 HIS B 59 PHE 0.014 0.002 PHE R 392 TYR 0.016 0.002 TYR C 106 ARG 0.003 0.000 ARG B 45 *********************** 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: 25 poor density : 66 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6565 (m100) cc_final: 0.6219 (m100) REVERT: C 79 LEU cc_start: 0.9172 (tp) cc_final: 0.8859 (tp) REVERT: D 29 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6829 (t80) REVERT: R 417 LYS cc_start: 0.8809 (mttt) cc_final: 0.8512 (mmtm) outliers start: 25 outliers final: 23 residues processed: 82 average time/residue: 0.4326 time to fit residues: 44.9298 Evaluate side-chains 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 81 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4581 r_free = 0.4581 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.095341 restraints weight = 90060.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.098186 restraints weight = 45174.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.099885 restraints weight = 28114.341| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.5231 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= 0.215 Angle : 0.569 6.511 7616 Z= 0.308 Chirality : 0.044 0.186 793 Planarity : 0.005 0.120 996 Dihedral : 5.668 36.006 789 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.55 % Favored : 89.73 % Rotamer: Outliers : 3.97 % Allowed : 14.16 % 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: -1.91 (0.32), residues: 691 helix: -4.68 (0.81), residues: 8 sheet: -0.35 (0.33), residues: 246 loop : -1.84 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.004 0.002 HIS C 103 PHE 0.011 0.002 PHE R 429 TYR 0.013 0.001 TYR D 114 ARG 0.002 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 91 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6508 (m100) cc_final: 0.6088 (m100) REVERT: C 79 LEU cc_start: 0.9244 (tp) cc_final: 0.8966 (tp) REVERT: D 29 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6750 (t80) REVERT: R 383 SER cc_start: 0.4308 (OUTLIER) cc_final: 0.3857 (t) REVERT: R 417 LYS cc_start: 0.8769 (mttt) cc_final: 0.8494 (mmtm) outliers start: 23 outliers final: 21 residues processed: 83 average time/residue: 0.4252 time to fit residues: 44.6696 Evaluate side-chains 90 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 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 95 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 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: 4.9990 chunk 5 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** D 74 ASN ** R 519 HIS ** 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 = 0.4530 r_free = 0.4530 target = 0.104398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.092281 restraints weight = 93086.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.095022 restraints weight = 47367.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.096661 restraints weight = 29743.839| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 5618 Z= 0.322 Angle : 0.653 6.531 7616 Z= 0.359 Chirality : 0.045 0.197 793 Planarity : 0.006 0.118 996 Dihedral : 6.135 39.028 789 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.59 % Favored : 86.69 % Rotamer: Outliers : 4.32 % Allowed : 13.99 % 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: -2.11 (0.32), residues: 691 helix: -4.78 (0.73), residues: 8 sheet: -0.55 (0.34), residues: 235 loop : -1.91 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 436 HIS 0.007 0.002 HIS B 59 PHE 0.019 0.002 PHE R 392 TYR 0.020 0.002 TYR B 112 ARG 0.003 0.001 ARG A 75 *********************** 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 93 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6516 (m100) cc_final: 0.6141 (m100) REVERT: D 72 ARG cc_start: 0.5949 (tmm-80) cc_final: 0.5545 (tmm-80) REVERT: R 417 LYS cc_start: 0.8811 (mttt) cc_final: 0.8574 (mmtm) outliers start: 25 outliers final: 22 residues processed: 84 average time/residue: 0.4240 time to fit residues: 45.1473 Evaluate side-chains 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 95 TYR 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 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: 0.3980 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 439 ASN R 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.095756 restraints weight = 90248.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.098603 restraints weight = 45267.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.100314 restraints weight = 28059.371| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.5609 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= 0.196 Angle : 0.572 6.334 7616 Z= 0.308 Chirality : 0.043 0.180 793 Planarity : 0.005 0.118 996 Dihedral : 5.657 34.997 789 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.55 % Favored : 89.58 % Rotamer: Outliers : 3.11 % Allowed : 15.37 % 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: -1.98 (0.32), residues: 691 helix: -4.38 (1.10), residues: 8 sheet: -0.46 (0.33), residues: 246 loop : -1.85 (0.30), residues: 437 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 0.010 0.002 PHE R 429 TYR 0.013 0.001 TYR D 114 ARG 0.003 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 89 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 TRP cc_start: 0.6886 (m100) cc_final: 0.6075 (m100) REVERT: D 72 ARG cc_start: 0.5770 (tmm-80) cc_final: 0.5204 (tmm-80) REVERT: R 417 LYS cc_start: 0.8785 (mttt) cc_final: 0.8530 (mmtm) outliers start: 18 outliers final: 17 residues processed: 83 average time/residue: 0.4396 time to fit residues: 45.8354 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 : 0.848 ------------------------------------------------------------------------------- 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 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 95 TYR Chi-restraints excluded: chain C residue 106 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.105049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.091772 restraints weight = 79015.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.094912 restraints weight = 39366.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.096734 restraints weight = 24071.354| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 5618 Z= 0.289 Angle : 0.624 5.512 7616 Z= 0.342 Chirality : 0.044 0.193 793 Planarity : 0.005 0.116 996 Dihedral : 5.969 40.140 789 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.01 % Favored : 87.12 % Rotamer: Outliers : 3.11 % Allowed : 15.72 % 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: -2.05 (0.32), residues: 691 helix: None (None), residues: 0 sheet: -0.62 (0.33), residues: 250 loop : -1.91 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 436 HIS 0.005 0.002 HIS B 59 PHE 0.014 0.002 PHE R 392 TYR 0.015 0.002 TYR D 114 ARG 0.003 0.001 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4722.95 seconds wall clock time: 83 minutes 54.42 seconds (5034.42 seconds total)