Starting phenix.real_space_refine on Thu Mar 6 03:23:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1b_41806/03_2025/8u1b_41806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1b_41806/03_2025/8u1b_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_41806/03_2025/8u1b_41806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1b_41806/03_2025/8u1b_41806.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1b_41806/03_2025/8u1b_41806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1b_41806/03_2025/8u1b_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-5624/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: 3.79, per 1000 atoms: 0.83 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: 1.09 Conformation dependent library (CDL) restraints added in 574.3 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: 0.60 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: 1.30 Time building geometry restraints manager: 1.32 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: 1.320 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- 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 : 0.474 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1342 time to fit residues: 13.8876 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 : 0.466 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124243 restraints weight = 8009.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127306 restraints weight = 5375.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129447 restraints weight = 3985.308| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.517 Fit side-chains REVERT: A 1955 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5385 (tt) REVERT: A 2155 MET cc_start: 0.8016 (ptm) cc_final: 0.7739 (ptm) REVERT: A 2211 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7365 (pptt) REVERT: A 2459 MET cc_start: 0.8126 (pmm) cc_final: 0.7703 (pmm) REVERT: C 103 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8156 (ptmt) outliers start: 30 outliers final: 10 residues processed: 107 average time/residue: 0.1711 time to fit residues: 23.2724 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 : 0.484 ------------------------------------------------------------------------------- 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 46 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130961 restraints weight = 7666.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133954 restraints weight = 4952.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136113 restraints weight = 3570.394| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1317 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= 0.217 Angle : 0.674 11.952 6334 Z= 0.334 Chirality : 0.043 0.140 782 Planarity : 0.004 0.047 789 Dihedral : 5.167 22.226 629 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.58 % Favored : 91.08 % Rotamer: Outliers : 6.24 % Allowed : 34.51 % Favored : 59.25 % 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: -1.67 (0.35), residues: 583 helix: -0.45 (0.38), residues: 197 sheet: -1.04 (0.52), residues: 84 loop : -1.56 (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 0.017 0.002 PHE C 83 TYR 0.011 0.001 TYR A2006 ARG 0.006 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 112 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.472 Fit side-chains REVERT: A 1955 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5413 (tt) REVERT: A 2117 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: A 2243 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8233 (t0) REVERT: A 2276 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: C 103 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8197 (ptmt) outliers start: 30 outliers final: 14 residues processed: 106 average time/residue: 0.1509 time to fit residues: 20.6821 Evaluate side-chains 93 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 16 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.149698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128348 restraints weight = 7899.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131662 restraints weight = 5193.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133842 restraints weight = 3780.365| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4656 Z= 0.192 Angle : 0.642 11.598 6334 Z= 0.318 Chirality : 0.043 0.140 782 Planarity : 0.004 0.038 789 Dihedral : 4.969 19.573 629 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.23 % Favored : 91.42 % Rotamer: Outliers : 6.86 % Allowed : 35.34 % 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: -1.66 (0.35), residues: 583 helix: -0.50 (0.37), residues: 196 sheet: -1.08 (0.50), residues: 93 loop : -1.49 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2214 HIS 0.004 0.001 HIS C 54 PHE 0.018 0.001 PHE C 83 TYR 0.011 0.001 TYR A2006 ARG 0.004 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 113 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.524 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5703 (tt) REVERT: A 2117 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: A 2276 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5662 (tm-30) REVERT: A 2459 MET cc_start: 0.8210 (pmm) cc_final: 0.7226 (pmm) outliers start: 33 outliers final: 18 residues processed: 107 average time/residue: 0.1518 time to fit residues: 21.1421 Evaluate side-chains 92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 2335 LEU 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 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 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.149245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127862 restraints weight = 8028.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131190 restraints weight = 5247.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133545 restraints weight = 3817.032| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1700 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 : 0.651 11.109 6334 Z= 0.323 Chirality : 0.043 0.157 782 Planarity : 0.004 0.037 789 Dihedral : 4.958 19.494 629 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.23 % Favored : 91.42 % Rotamer: Outliers : 6.44 % Allowed : 35.97 % 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: -1.68 (0.35), residues: 583 helix: -0.51 (0.37), residues: 198 sheet: -0.99 (0.50), residues: 92 loop : -1.55 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2214 HIS 0.004 0.001 HIS C 54 PHE 0.010 0.001 PHE A2181 TYR 0.010 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 107 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.467 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5925 (tt) REVERT: A 2117 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: A 2276 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5793 (tm-30) REVERT: A 2315 MET cc_start: 0.6941 (tpp) cc_final: 0.6701 (mmt) REVERT: A 2326 PHE cc_start: 0.7502 (m-10) cc_final: 0.7296 (m-10) outliers start: 31 outliers final: 19 residues processed: 102 average time/residue: 0.1432 time to fit residues: 19.1545 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 53 LEU Chi-restraints excluded: chain C residue 81 TYR 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 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.149064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129483 restraints weight = 7732.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132335 restraints weight = 5143.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134434 restraints weight = 3784.199| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4656 Z= 0.242 Angle : 0.664 11.250 6334 Z= 0.331 Chirality : 0.043 0.147 782 Planarity : 0.004 0.037 789 Dihedral : 5.012 19.819 629 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.92 % Favored : 90.74 % Rotamer: Outliers : 6.44 % Allowed : 35.97 % 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: -1.73 (0.35), residues: 583 helix: -0.64 (0.37), residues: 204 sheet: -0.99 (0.53), residues: 88 loop : -1.53 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2214 HIS 0.004 0.001 HIS A2206 PHE 0.017 0.002 PHE C 83 TYR 0.009 0.001 TYR A2006 ARG 0.004 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 113 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.530 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5975 (tt) REVERT: A 2117 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: A 2276 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5732 (tm-30) outliers start: 31 outliers final: 23 residues processed: 107 average time/residue: 0.1372 time to fit residues: 19.2913 Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 124 LEU 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 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.149434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129366 restraints weight = 7698.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132334 restraints weight = 5034.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134321 restraints weight = 3662.542| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4656 Z= 0.242 Angle : 0.667 11.436 6334 Z= 0.335 Chirality : 0.044 0.144 782 Planarity : 0.004 0.037 789 Dihedral : 5.038 21.101 629 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.75 % Favored : 90.91 % Rotamer: Outliers : 6.86 % Allowed : 35.55 % 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: -1.76 (0.35), residues: 583 helix: -0.67 (0.37), residues: 204 sheet: -1.04 (0.54), residues: 89 loop : -1.52 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A2214 HIS 0.004 0.001 HIS A2206 PHE 0.011 0.002 PHE A2181 TYR 0.009 0.001 TYR A2006 ARG 0.003 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 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.480 Fit side-chains REVERT: A 1955 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5812 (tt) REVERT: A 2112 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7604 (mptt) REVERT: A 2117 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: A 2276 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5796 (tm-30) outliers start: 33 outliers final: 25 residues processed: 103 average time/residue: 0.1490 time to fit residues: 19.9722 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 86 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4074 > 50: distance: 80 - 85: 7.318 distance: 85 - 86: 24.230 distance: 86 - 87: 22.213 distance: 86 - 89: 16.417 distance: 87 - 88: 21.137 distance: 87 - 90: 8.519 distance: 90 - 91: 14.755 distance: 91 - 92: 16.683 distance: 91 - 94: 16.376 distance: 92 - 93: 27.594 distance: 92 - 95: 9.925 distance: 95 - 96: 9.519 distance: 96 - 97: 9.271 distance: 96 - 99: 5.958 distance: 97 - 98: 45.863 distance: 97 - 103: 22.206 distance: 99 - 100: 5.718 distance: 100 - 101: 8.714 distance: 100 - 102: 12.786 distance: 103 - 104: 15.556 distance: 104 - 105: 46.064 distance: 104 - 107: 8.452 distance: 105 - 106: 5.370 distance: 105 - 111: 18.416 distance: 107 - 108: 10.620 distance: 107 - 109: 10.661 distance: 108 - 110: 14.841 distance: 111 - 112: 6.800 distance: 112 - 113: 11.766 distance: 112 - 115: 12.537 distance: 113 - 114: 14.358 distance: 113 - 116: 14.985 distance: 117 - 118: 5.344 distance: 117 - 120: 11.942 distance: 118 - 119: 8.370 distance: 118 - 123: 21.174 distance: 120 - 121: 17.691 distance: 120 - 122: 9.363 distance: 123 - 124: 8.428 distance: 124 - 125: 22.732 distance: 124 - 127: 15.805 distance: 125 - 126: 16.576 distance: 125 - 131: 20.555 distance: 127 - 128: 7.861 distance: 127 - 129: 12.608 distance: 128 - 130: 13.449 distance: 131 - 132: 14.763 distance: 132 - 133: 7.062 distance: 132 - 135: 5.863 distance: 133 - 134: 4.538 distance: 133 - 143: 11.203 distance: 135 - 136: 3.422 distance: 136 - 137: 3.495 distance: 136 - 138: 16.084 distance: 137 - 139: 5.960 distance: 138 - 140: 9.005 distance: 139 - 141: 11.604 distance: 140 - 141: 6.957 distance: 141 - 142: 6.265 distance: 143 - 144: 7.685 distance: 144 - 145: 8.762 distance: 144 - 147: 11.183 distance: 145 - 146: 9.613 distance: 145 - 151: 14.680 distance: 147 - 148: 5.432 distance: 148 - 149: 12.053 distance: 148 - 150: 16.563 distance: 151 - 152: 10.498 distance: 152 - 153: 19.858 distance: 152 - 155: 8.584 distance: 153 - 154: 8.063 distance: 153 - 162: 29.392 distance: 155 - 156: 9.754 distance: 156 - 157: 9.352 distance: 156 - 158: 9.689 distance: 157 - 159: 14.106 distance: 158 - 160: 9.345 distance: 159 - 161: 13.347 distance: 160 - 161: 16.316