Starting phenix.real_space_refine on Fri Dec 27 12:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1b_41806/12_2024/8u1b_41806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1b_41806/12_2024/8u1b_41806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1b_41806/12_2024/8u1b_41806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1b_41806/12_2024/8u1b_41806.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1b_41806/12_2024/8u1b_41806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1b_41806/12_2024/8u1b_41806.cif" } resolution = 3.7 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= 0.021 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2933 2.51 5 N 774 2.21 5 O 851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4584 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3496 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 446} Chain breaks: 11 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1088 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 3.52, per 1000 atoms: 0.77 Number of scatterers: 4584 At special positions: 0 Unit cell: (89.32, 81.2, 91.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 851 8.00 N 774 7.00 C 2933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A2452 " - pdb=" SG CYS A2492 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 577.9 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 35.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 1956 through 1961 Processing helix chain 'A' and resid 1967 through 1988 removed outlier: 3.672A pdb=" N ARG A1973 " --> pdb=" O THR A1969 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A1974 " --> pdb=" O LEU A1970 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A1975 " --> pdb=" O GLN A1971 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU A1976 " --> pdb=" O HIS A1972 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A1984 " --> pdb=" O ASP A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1996 through 2000 Processing helix chain 'A' and resid 2053 through 2068 removed outlier: 3.695A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A2058 " --> pdb=" O ALA A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2107 through 2115 removed outlier: 4.016A pdb=" N LYS A2112 " --> pdb=" O GLU A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 Processing helix chain 'A' and resid 2208 through 2211 Processing helix chain 'A' and resid 2276 through 2280 removed outlier: 4.016A pdb=" N VAL A2280 " --> pdb=" O ASP A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2344 removed outlier: 3.818A pdb=" N THR A2340 " --> pdb=" O GLU A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2394 Processing helix chain 'A' and resid 2499 through 2521 Processing helix chain 'C' and resid 17 through 27 removed outlier: 3.817A pdb=" N ARG C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.587A pdb=" N ASP C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.741A pdb=" N LYS C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 150 through 158 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.607A pdb=" N ALA C 164 " --> pdb=" O ASN C 160 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2142 through 2145 removed outlier: 3.524A pdb=" N MET A2459 " --> pdb=" O LEU A2471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2154 through 2156 removed outlier: 3.844A pdb=" N CYS A2154 " --> pdb=" O GLY A2170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 3.982A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A2214 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A2212 " --> pdb=" O LEU A2207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A2217 " --> pdb=" O LEU A2225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2247 through 2249 Processing sheet with id=AA5, first strand: chain 'A' and resid 2272 through 2274 removed outlier: 3.776A pdb=" N ILE A2274 " --> pdb=" O LYS A2289 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS A2289 " --> pdb=" O ILE A2274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2304 through 2305 removed outlier: 4.070A pdb=" N GLY A2317 " --> pdb=" O PHE A2324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.861A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL A2359 " --> pdb=" O ALA A2362 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA A2362 " --> pdb=" O VAL A2359 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A2365 " --> pdb=" O GLU A2374 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A2374 " --> pdb=" O ILE A2365 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP A2377 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A2383 " --> pdb=" O ASP A2377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2417 through 2419 169 hydrogen bonds defined for protein. 438 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: 1.22 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1277 1.33 - 1.45: 676 1.45 - 1.57: 2666 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 4656 Sorted by residual: bond pdb=" CA ARG C 33 " pdb=" C ARG C 33 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.08e-02 8.57e+03 5.07e+00 bond pdb=" CA VAL C 32 " pdb=" CB VAL C 32 " ideal model delta sigma weight residual 1.540 1.565 -0.024 1.36e-02 5.41e+03 3.24e+00 bond pdb=" C GLU C 31 " pdb=" O GLU C 31 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.09e+00 bond pdb=" C ARG C 33 " pdb=" O ARG C 33 " ideal model delta sigma weight residual 1.233 1.214 0.019 1.12e-02 7.97e+03 2.73e+00 bond pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.27e-02 6.20e+03 1.82e+00 ... (remaining 4651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 6226 2.43 - 4.86: 87 4.86 - 7.28: 12 7.28 - 9.71: 7 9.71 - 12.14: 2 Bond angle restraints: 6334 Sorted by residual: angle pdb=" N ARG C 33 " pdb=" CA ARG C 33 " pdb=" C ARG C 33 " ideal model delta sigma weight residual 107.32 119.46 -12.14 1.65e+00 3.67e-01 5.41e+01 angle pdb=" N ASP C 30 " pdb=" CA ASP C 30 " pdb=" C ASP C 30 " ideal model delta sigma weight residual 111.36 118.53 -7.17 1.09e+00 8.42e-01 4.32e+01 angle pdb=" N VAL A2107 " pdb=" CA VAL A2107 " pdb=" C VAL A2107 " ideal model delta sigma weight residual 112.12 106.79 5.33 8.40e-01 1.42e+00 4.02e+01 angle pdb=" N LEU C 86 " pdb=" CA LEU C 86 " pdb=" C LEU C 86 " ideal model delta sigma weight residual 114.04 106.70 7.34 1.24e+00 6.50e-01 3.51e+01 angle pdb=" C ARG C 33 " pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " ideal model delta sigma weight residual 111.70 104.87 6.83 1.31e+00 5.83e-01 2.72e+01 ... (remaining 6329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 2351 18.05 - 36.09: 309 36.09 - 54.14: 77 54.14 - 72.19: 15 72.19 - 90.24: 7 Dihedral angle restraints: 2759 sinusoidal: 1005 harmonic: 1754 Sorted by residual: dihedral pdb=" CB CYS A2452 " pdb=" SG CYS A2452 " pdb=" SG CYS A2492 " pdb=" CB CYS A2492 " ideal model delta sinusoidal sigma weight residual 93.00 179.37 -86.37 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" C VAL C 32 " pdb=" N VAL C 32 " pdb=" CA VAL C 32 " pdb=" CB VAL C 32 " ideal model delta harmonic sigma weight residual -122.00 -139.19 17.19 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" N VAL C 32 " pdb=" C VAL C 32 " pdb=" CA VAL C 32 " pdb=" CB VAL C 32 " ideal model delta harmonic sigma weight residual 123.40 137.58 -14.18 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 2756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 753 0.104 - 0.208: 28 0.208 - 0.313: 0 0.313 - 0.417: 0 0.417 - 0.521: 1 Chirality restraints: 782 Sorted by residual: chirality pdb=" CA VAL C 32 " pdb=" N VAL C 32 " pdb=" C VAL C 32 " pdb=" CB VAL C 32 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CA ARG C 33 " pdb=" N ARG C 33 " pdb=" C ARG C 33 " pdb=" CB ARG C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA ASP C 30 " pdb=" N ASP C 30 " pdb=" C ASP C 30 " pdb=" CB ASP C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 779 not shown) Planarity restraints: 789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A2104 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A2105 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A2105 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2105 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2214 " 0.014 2.00e-02 2.50e+03 1.37e-02 4.70e+00 pdb=" CG TRP A2214 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A2214 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A2214 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A2214 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A2214 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2214 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2214 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2214 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A2214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 31 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C GLU C 31 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU C 31 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C 32 " -0.010 2.00e-02 2.50e+03 ... (remaining 786 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 242 2.72 - 3.27: 4735 3.27 - 3.81: 7432 3.81 - 4.36: 8753 4.36 - 4.90: 14867 Nonbonded interactions: 36029 Sorted by model distance: nonbonded pdb=" OG1 THR C 150 " pdb=" OD1 ASP C 153 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR A2267 " pdb=" OD1 ASP A2269 " model vdw 2.198 3.040 nonbonded pdb=" O GLY A2430 " pdb=" OG SER A2454 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASN A2295 " pdb=" OG SER A2297 " model vdw 2.211 3.040 nonbonded pdb=" NE2 HIS C 54 " pdb=" O PHE C 83 " model vdw 2.222 3.120 ... (remaining 36024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 0.031 4656 Z= 0.214 Angle : 0.753 12.139 6334 Z= 0.411 Chirality : 0.047 0.521 782 Planarity : 0.004 0.062 789 Dihedral : 17.967 90.235 1614 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.06 % Favored : 91.42 % Rotamer: Outliers : 0.21 % Allowed : 37.21 % Favored : 62.58 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.36), residues: 583 helix: -0.73 (0.37), residues: 200 sheet: -0.12 (0.59), residues: 80 loop : -1.43 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A2214 HIS 0.002 0.001 HIS C 61 PHE 0.008 0.001 PHE A2181 TYR 0.013 0.001 TYR A2189 ARG 0.005 0.000 ARG A2122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.526 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1482 time to fit residues: 15.1882 Evaluate side-chains 69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4656 Z= 0.320 Angle : 0.718 10.186 6334 Z= 0.363 Chirality : 0.045 0.145 782 Planarity : 0.005 0.055 789 Dihedral : 5.417 24.553 629 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.26 % Favored : 90.22 % Rotamer: Outliers : 6.24 % Allowed : 31.19 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.72 (0.35), residues: 583 helix: -0.52 (0.38), residues: 194 sheet: -0.94 (0.52), residues: 84 loop : -1.59 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2214 HIS 0.006 0.001 HIS C 54 PHE 0.016 0.002 PHE A2181 TYR 0.008 0.001 TYR A1984 ARG 0.001 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.501 Fit side-chains REVERT: A 1955 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5327 (tt) REVERT: A 2155 MET cc_start: 0.8066 (ptm) cc_final: 0.7743 (ptm) REVERT: A 2211 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7472 (pptt) REVERT: A 2459 MET cc_start: 0.8048 (pmm) cc_final: 0.7574 (pmm) REVERT: C 103 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8109 (ptmt) outliers start: 30 outliers final: 10 residues processed: 107 average time/residue: 0.1745 time to fit residues: 23.6535 Evaluate side-chains 83 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2340 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1977 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4656 Z= 0.191 Angle : 0.667 12.015 6334 Z= 0.328 Chirality : 0.043 0.137 782 Planarity : 0.004 0.046 789 Dihedral : 5.073 22.008 629 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.23 % Favored : 91.42 % Rotamer: Outliers : 6.03 % Allowed : 33.68 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.64 (0.35), residues: 583 helix: -0.44 (0.37), residues: 197 sheet: -1.02 (0.52), residues: 84 loop : -1.52 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2214 HIS 0.004 0.001 HIS C 54 PHE 0.018 0.001 PHE C 83 TYR 0.012 0.001 TYR A2006 ARG 0.008 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.517 Fit side-chains REVERT: A 1955 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5471 (tt) REVERT: A 2117 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: A 2243 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8203 (t0) REVERT: A 2276 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5927 (tm-30) REVERT: A 2315 MET cc_start: 0.6907 (tpp) cc_final: 0.6698 (tpp) REVERT: C 103 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8126 (ptmt) outliers start: 29 outliers final: 13 residues processed: 105 average time/residue: 0.1591 time to fit residues: 21.3932 Evaluate side-chains 93 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2243 ASP Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4656 Z= 0.247 Angle : 0.668 11.311 6334 Z= 0.333 Chirality : 0.043 0.147 782 Planarity : 0.004 0.039 789 Dihedral : 5.124 21.150 629 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.09 % Favored : 90.57 % Rotamer: Outliers : 6.65 % Allowed : 34.51 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.74 (0.35), residues: 583 helix: -0.49 (0.37), residues: 195 sheet: -1.16 (0.50), residues: 93 loop : -1.57 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2214 HIS 0.004 0.001 HIS C 54 PHE 0.015 0.002 PHE C 83 TYR 0.009 0.001 TYR A2006 ARG 0.005 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.551 Fit side-chains REVERT: A 1955 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5361 (tt) REVERT: A 2117 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: A 2276 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5790 (tm-30) REVERT: A 2458 MET cc_start: 0.7486 (ptt) cc_final: 0.6929 (ptt) REVERT: A 2459 MET cc_start: 0.8112 (pmm) cc_final: 0.7101 (pmm) outliers start: 32 outliers final: 16 residues processed: 104 average time/residue: 0.1555 time to fit residues: 20.9385 Evaluate side-chains 91 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4656 Z= 0.239 Angle : 0.656 10.987 6334 Z= 0.327 Chirality : 0.043 0.160 782 Planarity : 0.004 0.038 789 Dihedral : 5.075 19.721 629 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.06 % Favored : 91.60 % Rotamer: Outliers : 7.28 % Allowed : 35.14 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.35), residues: 583 helix: -0.52 (0.37), residues: 197 sheet: -1.14 (0.50), residues: 92 loop : -1.63 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A2214 HIS 0.004 0.001 HIS C 54 PHE 0.011 0.001 PHE A2181 TYR 0.009 0.001 TYR A2006 ARG 0.004 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.537 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5640 (tt) REVERT: A 2117 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: A 2276 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: A 2459 MET cc_start: 0.8147 (pmm) cc_final: 0.6983 (pmm) outliers start: 35 outliers final: 23 residues processed: 107 average time/residue: 0.1535 time to fit residues: 21.4385 Evaluate side-chains 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2201 CYS Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2517 LEU Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.1980 chunk 56 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4656 Z= 0.188 Angle : 0.658 11.896 6334 Z= 0.325 Chirality : 0.043 0.155 782 Planarity : 0.004 0.037 789 Dihedral : 4.901 19.734 629 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.06 % Favored : 91.60 % Rotamer: Outliers : 6.03 % Allowed : 35.76 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.71 (0.35), residues: 583 helix: -0.49 (0.37), residues: 197 sheet: -1.11 (0.52), residues: 93 loop : -1.55 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2214 HIS 0.004 0.001 HIS C 127 PHE 0.007 0.001 PHE A2181 TYR 0.011 0.001 TYR A2006 ARG 0.003 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.554 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5815 (tt) REVERT: A 2117 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: A 2219 THR cc_start: 0.8693 (m) cc_final: 0.8486 (p) REVERT: A 2276 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5761 (tm-30) outliers start: 29 outliers final: 21 residues processed: 104 average time/residue: 0.1574 time to fit residues: 21.1292 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2201 CYS Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4656 Z= 0.236 Angle : 0.662 11.221 6334 Z= 0.329 Chirality : 0.043 0.143 782 Planarity : 0.004 0.037 789 Dihedral : 4.996 21.410 629 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.75 % Favored : 90.91 % Rotamer: Outliers : 6.44 % Allowed : 35.34 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.35), residues: 583 helix: -0.65 (0.37), residues: 203 sheet: -1.00 (0.54), residues: 88 loop : -1.55 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2214 HIS 0.004 0.001 HIS A2206 PHE 0.011 0.001 PHE A2181 TYR 0.009 0.001 TYR A2006 ARG 0.004 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.507 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5779 (tt) REVERT: A 2112 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7480 (mptt) REVERT: A 2117 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8131 (tp30) REVERT: A 2276 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5844 (tm-30) REVERT: A 2315 MET cc_start: 0.6686 (mmt) cc_final: 0.6451 (tpp) outliers start: 31 outliers final: 23 residues processed: 103 average time/residue: 0.1501 time to fit residues: 19.9596 Evaluate side-chains 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2112 LYS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4656 Z= 0.295 Angle : 0.688 11.642 6334 Z= 0.344 Chirality : 0.044 0.149 782 Planarity : 0.004 0.037 789 Dihedral : 5.224 22.894 629 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.75 % Favored : 90.91 % Rotamer: Outliers : 6.24 % Allowed : 35.34 % Favored : 58.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.84 (0.35), residues: 583 helix: -0.68 (0.37), residues: 203 sheet: -1.07 (0.53), residues: 88 loop : -1.62 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2214 HIS 0.004 0.001 HIS A2206 PHE 0.014 0.002 PHE A2181 TYR 0.008 0.001 TYR A2006 ARG 0.003 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.482 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5891 (tt) REVERT: A 2112 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7497 (mptt) REVERT: A 2117 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: A 2276 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5767 (tm-30) REVERT: A 2315 MET cc_start: 0.6858 (mmt) cc_final: 0.6512 (tpp) outliers start: 30 outliers final: 22 residues processed: 101 average time/residue: 0.1608 time to fit residues: 20.7975 Evaluate side-chains 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2112 LYS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 0.0270 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4656 Z= 0.212 Angle : 0.666 11.731 6334 Z= 0.330 Chirality : 0.043 0.142 782 Planarity : 0.004 0.035 789 Dihedral : 5.062 22.111 629 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.89 % Favored : 91.77 % Rotamer: Outliers : 5.82 % Allowed : 36.38 % Favored : 57.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.35), residues: 583 helix: -0.63 (0.37), residues: 203 sheet: -1.05 (0.51), residues: 94 loop : -1.59 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2214 HIS 0.003 0.001 HIS C 127 PHE 0.009 0.001 PHE A2181 TYR 0.010 0.001 TYR A2006 ARG 0.003 0.000 ARG A2514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.534 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5850 (tt) REVERT: A 2112 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7456 (mptt) REVERT: A 2117 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8059 (tp30) REVERT: A 2276 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5477 (tm-30) REVERT: A 2315 MET cc_start: 0.6914 (mmt) cc_final: 0.5730 (mpp) outliers start: 28 outliers final: 22 residues processed: 97 average time/residue: 0.1609 time to fit residues: 20.4674 Evaluate side-chains 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2112 LYS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4656 Z= 0.206 Angle : 0.656 11.369 6334 Z= 0.325 Chirality : 0.043 0.141 782 Planarity : 0.004 0.034 789 Dihedral : 4.984 22.171 629 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.23 % Favored : 91.42 % Rotamer: Outliers : 5.82 % Allowed : 36.59 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.69 (0.35), residues: 583 helix: -0.55 (0.37), residues: 203 sheet: -1.00 (0.51), residues: 94 loop : -1.54 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2214 HIS 0.003 0.001 HIS C 127 PHE 0.009 0.001 PHE A2181 TYR 0.010 0.001 TYR A2006 ARG 0.003 0.000 ARG A2514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.560 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5805 (tt) REVERT: A 2112 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7476 (mptt) REVERT: A 2117 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: A 2276 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5716 (tm-30) REVERT: A 2315 MET cc_start: 0.6938 (mmt) cc_final: 0.5769 (mpp) REVERT: A 2459 MET cc_start: 0.8116 (pmm) cc_final: 0.7046 (pmm) outliers start: 28 outliers final: 22 residues processed: 102 average time/residue: 0.1699 time to fit residues: 22.0577 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1959 LEU Chi-restraints excluded: chain A residue 2006 TYR Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2112 LYS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2140 LEU Chi-restraints excluded: chain A residue 2189 TYR Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2211 LYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2281 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2390 VAL Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2506 ASN Chi-restraints excluded: chain A residue 2517 LEU Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.0060 chunk 20 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.151967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132774 restraints weight = 7544.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135699 restraints weight = 4955.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137841 restraints weight = 3610.664| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4656 Z= 0.190 Angle : 0.647 10.871 6334 Z= 0.321 Chirality : 0.043 0.139 782 Planarity : 0.003 0.035 789 Dihedral : 4.874 21.700 629 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.72 % Favored : 91.94 % Rotamer: Outliers : 5.82 % Allowed : 36.80 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.64 (0.35), residues: 583 helix: -0.54 (0.37), residues: 203 sheet: -0.83 (0.53), residues: 93 loop : -1.54 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2214 HIS 0.005 0.001 HIS A1977 PHE 0.008 0.001 PHE A2181 TYR 0.010 0.001 TYR A2006 ARG 0.002 0.000 ARG A2514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.76 seconds wall clock time: 25 minutes 57.26 seconds (1557.26 seconds total)