Starting phenix.real_space_refine on Wed Feb 12 16:58:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jz3_22529/02_2025/7jz3_22529_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jz3_22529/02_2025/7jz3_22529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jz3_22529/02_2025/7jz3_22529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jz3_22529/02_2025/7jz3_22529.map" model { file = "/net/cci-nas-00/data/ceres_data/7jz3_22529/02_2025/7jz3_22529_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jz3_22529/02_2025/7jz3_22529_neut.cif" } resolution = 2.56 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 ------------------------------------------------------------------------------- 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= 0.212 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 9 5.16 5 C 5097 2.51 5 N 1374 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8142 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Restraints were copied for chains: C, B Time building chain proxies: 4.40, per 1000 atoms: 0.54 Number of scatterers: 8142 At special positions: 0 Unit cell: (93.96, 92.88, 71.28, 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 9 16.00 O 1662 8.00 N 1374 7.00 C 5097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 6.4% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 4 through 5 current: chain 'B' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL B 75 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 59 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 73 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 61 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER B 71 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 91 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN B 93 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 126 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG B 217 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 244 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B 254 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 245 " --> pdb=" O TRP B 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP B 252 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 255 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 283 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 281 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 279 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY B 282 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 293 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 4 through 5 current: chain 'C' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL C 75 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 59 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR C 73 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN C 61 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 71 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 91 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 93 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN C 126 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG C 217 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 244 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C 254 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR C 245 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP C 252 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 255 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 283 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 281 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 279 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY C 282 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP C 293 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 5 current: chain 'A' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL A 75 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 59 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 73 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN A 61 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 71 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 91 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 93 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 126 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG A 217 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 244 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN A 254 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 245 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP A 252 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 255 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 283 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 281 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 279 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 265 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY A 282 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 293 " --> pdb=" O GLY A 282 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1089 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: 2.30 Time building geometry restraints manager: 2.37 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: 2154 1.33 - 1.45: 1915 1.45 - 1.57: 4232 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 8319 Sorted by residual: bond pdb=" CA ASN C 133 " pdb=" CB ASN C 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.37e+00 bond pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.26e+00 bond pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.55e-02 4.16e+03 6.21e+00 bond pdb=" N ASN C 133 " pdb=" CA ASN C 133 " ideal model delta sigma weight residual 1.455 1.427 0.028 1.22e-02 6.72e+03 5.39e+00 bond pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta sigma weight residual 1.455 1.428 0.028 1.22e-02 6.72e+03 5.11e+00 ... (remaining 8314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 10773 1.39 - 2.79: 428 2.79 - 4.18: 53 4.18 - 5.57: 8 5.57 - 6.97: 3 Bond angle restraints: 11265 Sorted by residual: angle pdb=" N VAL B 29 " pdb=" CA VAL B 29 " pdb=" C VAL B 29 " ideal model delta sigma weight residual 113.53 109.81 3.72 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N VAL C 29 " pdb=" CA VAL C 29 " pdb=" C VAL C 29 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.42e+01 angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" N GLY C 138 " pdb=" CA GLY C 138 " pdb=" C GLY C 138 " ideal model delta sigma weight residual 115.32 119.34 -4.02 1.38e+00 5.25e-01 8.49e+00 angle pdb=" N GLY B 138 " pdb=" CA GLY B 138 " pdb=" C GLY B 138 " ideal model delta sigma weight residual 115.32 119.33 -4.01 1.38e+00 5.25e-01 8.43e+00 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 4233 16.34 - 32.69: 365 32.69 - 49.03: 88 49.03 - 65.37: 15 65.37 - 81.71: 6 Dihedral angle restraints: 4707 sinusoidal: 1791 harmonic: 2916 Sorted by residual: dihedral pdb=" CA GLN A 237 " pdb=" CB GLN A 237 " pdb=" CG GLN A 237 " pdb=" CD GLN A 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.89 50.89 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " pdb=" CD GLN B 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.88 50.88 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN C 237 " pdb=" CB GLN C 237 " pdb=" CG GLN C 237 " pdb=" CD GLN C 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.86 50.86 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 4704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 722 0.037 - 0.073: 279 0.073 - 0.110: 91 0.110 - 0.147: 30 0.147 - 0.183: 6 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PHE C 136 " pdb=" N PHE C 136 " pdb=" C PHE C 136 " pdb=" CB PHE C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE B 136 " pdb=" N PHE B 136 " pdb=" C PHE B 136 " pdb=" CB PHE B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA PHE A 136 " pdb=" N PHE A 136 " pdb=" C PHE A 136 " pdb=" CB PHE A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1125 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 84 " -0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CG ASP A 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 84 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" CG ASP C 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP C 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 84 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" CG ASP B 84 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP B 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 7936 3.29 - 3.82: 13672 3.82 - 4.36: 17117 4.36 - 4.90: 30181 Nonbonded interactions: 69744 Sorted by model distance: nonbonded pdb=" NE2 GLN B 237 " pdb=" OG1 THR B 239 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN C 237 " pdb=" OG1 THR C 239 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN A 237 " pdb=" OG1 THR A 239 " model vdw 2.211 3.120 nonbonded pdb=" OD2 ASP A 89 " pdb=" ND2 ASN A 93 " model vdw 2.288 3.120 nonbonded pdb=" OD2 ASP B 89 " pdb=" ND2 ASN B 93 " model vdw 2.289 3.120 ... (remaining 69739 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.600 Find NCS groups from input model: 0.140 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 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 0.039 8319 Z= 0.213 Angle : 0.623 6.968 11265 Z= 0.384 Chirality : 0.046 0.183 1128 Planarity : 0.003 0.038 1530 Dihedral : 13.643 81.714 2913 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.09 % Allowed : 7.27 % Favored : 91.64 % 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: -2.54 (0.23), residues: 1032 helix: -2.59 (0.66), residues: 42 sheet: -0.80 (0.20), residues: 561 loop : -2.78 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 56 HIS 0.002 0.001 HIS C 21 PHE 0.011 0.002 PHE B 269 TYR 0.012 0.001 TYR B 58 ARG 0.001 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.5712 (mttm) cc_final: 0.5058 (mptt) REVERT: B 291 ASP cc_start: 0.5276 (m-30) cc_final: 0.4920 (t0) REVERT: C 281 LYS cc_start: 0.5715 (mttm) cc_final: 0.5460 (mttm) REVERT: C 310 MET cc_start: 0.7723 (tpt) cc_final: 0.7399 (tpt) REVERT: A 281 LYS cc_start: 0.5722 (mttm) cc_final: 0.5054 (mptt) REVERT: A 291 ASP cc_start: 0.5277 (m-30) cc_final: 0.4989 (t0) REVERT: A 319 ASN cc_start: 0.5859 (t0) cc_final: 0.5251 (t0) outliers start: 9 outliers final: 5 residues processed: 203 average time/residue: 0.8763 time to fit residues: 192.2272 Evaluate side-chains 156 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 21 HIS B 45 GLN B 61 GLN B 83 GLN B 144 ASN B 231 ASN B 237 GLN B 264 GLN C 21 HIS C 45 GLN C 61 GLN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN A 9 ASN A 21 HIS A 45 GLN A 61 GLN A 144 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 264 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.249873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.238338 restraints weight = 9726.989| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 1.78 r_work: 0.4680 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4589 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 8319 Z= 0.488 Angle : 0.910 12.523 11265 Z= 0.487 Chirality : 0.054 0.159 1128 Planarity : 0.006 0.049 1530 Dihedral : 6.307 54.933 1171 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.30 % Allowed : 17.82 % Favored : 75.88 % 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: -2.76 (0.23), residues: 1032 helix: -2.66 (0.50), residues: 60 sheet: -0.72 (0.20), residues: 543 loop : -3.21 (0.23), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 252 HIS 0.002 0.001 HIS A 21 PHE 0.039 0.004 PHE C 40 TYR 0.026 0.003 TYR C 313 ARG 0.010 0.002 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 0.798 Fit side-chains REVERT: B 23 PHE cc_start: 0.4299 (m-80) cc_final: 0.3477 (m-80) REVERT: B 178 ASP cc_start: 0.6829 (m-30) cc_final: 0.6546 (m-30) REVERT: B 189 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6856 (tm-30) REVERT: B 212 ILE cc_start: 0.7113 (pt) cc_final: 0.6844 (pt) REVERT: B 237 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5759 (tt0) REVERT: B 252 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.5647 (m-90) REVERT: B 281 LYS cc_start: 0.5319 (mttm) cc_final: 0.4154 (mttt) REVERT: C 27 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6901 (mmtp) REVERT: C 83 GLN cc_start: 0.7990 (pt0) cc_final: 0.7746 (pt0) REVERT: C 189 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6831 (tm-30) REVERT: C 217 ARG cc_start: 0.6083 (mtp85) cc_final: 0.5712 (mtp85) REVERT: C 219 GLU cc_start: 0.4913 (OUTLIER) cc_final: 0.3925 (mp0) REVERT: C 281 LYS cc_start: 0.5450 (mttm) cc_final: 0.4472 (mttt) REVERT: C 310 MET cc_start: 0.7904 (tpt) cc_final: 0.7597 (tpt) REVERT: A 50 LEU cc_start: 0.7639 (tm) cc_final: 0.7416 (tm) REVERT: A 73 THR cc_start: 0.7708 (p) cc_final: 0.7484 (t) REVERT: A 121 MET cc_start: 0.6987 (mmm) cc_final: 0.6644 (mmm) REVERT: A 189 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 281 LYS cc_start: 0.5610 (mttm) cc_final: 0.4454 (mptt) REVERT: A 287 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7205 (mtp85) outliers start: 52 outliers final: 21 residues processed: 207 average time/residue: 0.9507 time to fit residues: 212.0760 Evaluate side-chains 196 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 304 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.258820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.247384 restraints weight = 9729.223| |-----------------------------------------------------------------------------| r_work (start): 0.4789 rms_B_bonded: 1.81 r_work: 0.4746 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4659 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8319 Z= 0.206 Angle : 0.674 9.326 11265 Z= 0.360 Chirality : 0.047 0.150 1128 Planarity : 0.004 0.051 1530 Dihedral : 5.302 39.365 1170 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.73 % Allowed : 24.12 % Favored : 71.15 % 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: -2.34 (0.24), residues: 1032 helix: -1.95 (0.62), residues: 60 sheet: -0.60 (0.21), residues: 558 loop : -2.83 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 56 HIS 0.001 0.001 HIS A 21 PHE 0.022 0.002 PHE C 40 TYR 0.018 0.002 TYR A 98 ARG 0.005 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.5181 (mttm) cc_final: 0.4271 (mttp) REVERT: B 287 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6972 (mtp85) REVERT: B 319 ASN cc_start: 0.6757 (t0) cc_final: 0.6382 (t0) REVERT: C 27 LYS cc_start: 0.7518 (mptt) cc_final: 0.6763 (mmtp) REVERT: C 57 GLU cc_start: 0.7893 (tt0) cc_final: 0.7682 (tt0) REVERT: C 92 ARG cc_start: 0.6042 (ttt180) cc_final: 0.5666 (tpt170) REVERT: C 189 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6779 (tm-30) REVERT: C 219 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.3835 (mp0) REVERT: C 255 LYS cc_start: 0.6027 (mttt) cc_final: 0.5813 (mttp) REVERT: C 281 LYS cc_start: 0.5462 (mttm) cc_final: 0.4435 (mttp) REVERT: A 12 ASP cc_start: 0.5997 (p0) cc_final: 0.5680 (p0) REVERT: A 57 GLU cc_start: 0.7841 (tt0) cc_final: 0.7621 (tt0) REVERT: A 189 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6732 (tm-30) REVERT: A 255 LYS cc_start: 0.6115 (mttt) cc_final: 0.5723 (mttp) REVERT: A 281 LYS cc_start: 0.5610 (mttm) cc_final: 0.4409 (mptt) outliers start: 39 outliers final: 20 residues processed: 201 average time/residue: 0.8990 time to fit residues: 195.2264 Evaluate side-chains 184 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN B 148 GLN B 264 GLN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.254753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.243295 restraints weight = 9673.199| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 1.79 r_work: 0.4716 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4629 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8319 Z= 0.292 Angle : 0.725 9.579 11265 Z= 0.389 Chirality : 0.048 0.178 1128 Planarity : 0.004 0.057 1530 Dihedral : 5.215 18.753 1164 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.18 % Allowed : 24.48 % Favored : 69.33 % 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: -2.31 (0.24), residues: 1032 helix: -2.26 (0.59), residues: 60 sheet: -0.50 (0.21), residues: 552 loop : -2.85 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 56 HIS 0.002 0.001 HIS A 21 PHE 0.021 0.002 PHE C 40 TYR 0.021 0.002 TYR C 98 ARG 0.005 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: B 178 ASP cc_start: 0.6876 (m-30) cc_final: 0.6622 (m-30) REVERT: B 189 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6982 (tm-30) REVERT: B 281 LYS cc_start: 0.5268 (mttm) cc_final: 0.4169 (mttt) REVERT: B 319 ASN cc_start: 0.6974 (t0) cc_final: 0.6572 (t0) REVERT: C 27 LYS cc_start: 0.7453 (mptt) cc_final: 0.6735 (mmtp) REVERT: C 126 ASN cc_start: 0.7265 (m110) cc_final: 0.7008 (m-40) REVERT: C 170 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.5411 (ptp-170) REVERT: C 189 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6780 (tm-30) REVERT: C 219 GLU cc_start: 0.4811 (OUTLIER) cc_final: 0.3722 (mp0) REVERT: C 255 LYS cc_start: 0.5949 (mttt) cc_final: 0.5676 (mttp) REVERT: C 258 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.7011 (m110) REVERT: C 281 LYS cc_start: 0.5474 (mttm) cc_final: 0.4434 (mttt) REVERT: A 96 VAL cc_start: 0.6194 (OUTLIER) cc_final: 0.5908 (m) REVERT: A 255 LYS cc_start: 0.6032 (mttt) cc_final: 0.5663 (mttp) REVERT: A 281 LYS cc_start: 0.5730 (mttm) cc_final: 0.4549 (mptt) outliers start: 51 outliers final: 30 residues processed: 206 average time/residue: 0.9214 time to fit residues: 204.6162 Evaluate side-chains 195 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 304 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 126 ASN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.248168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.236426 restraints weight = 9603.445| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 1.79 r_work: 0.4669 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4581 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8319 Z= 0.500 Angle : 0.902 10.121 11265 Z= 0.485 Chirality : 0.054 0.235 1128 Planarity : 0.006 0.059 1530 Dihedral : 6.016 23.163 1164 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 8.73 % Allowed : 24.97 % Favored : 66.30 % 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: -2.70 (0.23), residues: 1032 helix: -2.75 (0.53), residues: 60 sheet: -0.62 (0.21), residues: 543 loop : -3.24 (0.23), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 252 HIS 0.004 0.002 HIS A 21 PHE 0.023 0.003 PHE C 40 TYR 0.027 0.003 TYR A 221 ARG 0.008 0.001 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: B 178 ASP cc_start: 0.6913 (m-30) cc_final: 0.6693 (m-30) REVERT: B 189 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 252 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.5535 (m-90) REVERT: B 281 LYS cc_start: 0.5357 (mttm) cc_final: 0.4245 (mptt) REVERT: C 27 LYS cc_start: 0.7616 (mptt) cc_final: 0.6863 (mmtp) REVERT: C 126 ASN cc_start: 0.7228 (m110) cc_final: 0.6968 (m-40) REVERT: C 170 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5622 (ptp-170) REVERT: C 189 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6829 (tm-30) REVERT: C 219 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.3869 (mp0) REVERT: C 258 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7086 (m110) REVERT: C 281 LYS cc_start: 0.5598 (mttm) cc_final: 0.4520 (mttt) REVERT: A 170 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5649 (ptp-170) REVERT: A 252 TRP cc_start: 0.7014 (OUTLIER) cc_final: 0.5268 (m-90) REVERT: A 281 LYS cc_start: 0.5661 (mttm) cc_final: 0.4740 (mttp) outliers start: 72 outliers final: 41 residues processed: 215 average time/residue: 0.9007 time to fit residues: 208.8612 Evaluate side-chains 208 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.254396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.242872 restraints weight = 9649.004| |-----------------------------------------------------------------------------| r_work (start): 0.4751 rms_B_bonded: 1.79 r_work: 0.4708 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4619 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8319 Z= 0.266 Angle : 0.726 9.577 11265 Z= 0.386 Chirality : 0.048 0.156 1128 Planarity : 0.004 0.058 1530 Dihedral : 5.360 20.667 1164 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 6.67 % Allowed : 27.03 % Favored : 66.30 % 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: -2.31 (0.24), residues: 1032 helix: -1.84 (0.76), residues: 42 sheet: -0.55 (0.21), residues: 549 loop : -2.81 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 56 HIS 0.002 0.001 HIS A 21 PHE 0.018 0.002 PHE C 40 TYR 0.021 0.002 TYR C 98 ARG 0.006 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.820 Fit side-chains REVERT: B 178 ASP cc_start: 0.6892 (m-30) cc_final: 0.6666 (m-30) REVERT: B 189 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 281 LYS cc_start: 0.5224 (mttm) cc_final: 0.4135 (mttt) REVERT: C 27 LYS cc_start: 0.7582 (mptt) cc_final: 0.6842 (mmtp) REVERT: C 57 GLU cc_start: 0.7879 (tt0) cc_final: 0.7672 (tt0) REVERT: C 73 THR cc_start: 0.7541 (t) cc_final: 0.7172 (m) REVERT: C 126 ASN cc_start: 0.7216 (m110) cc_final: 0.6979 (m-40) REVERT: C 170 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5473 (ptp-170) REVERT: C 189 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6761 (tm-30) REVERT: C 219 GLU cc_start: 0.4848 (OUTLIER) cc_final: 0.3760 (mp0) REVERT: C 258 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.7081 (m110) REVERT: C 281 LYS cc_start: 0.5522 (mttm) cc_final: 0.4508 (mttt) REVERT: A 12 ASP cc_start: 0.6088 (p0) cc_final: 0.5727 (p0) REVERT: A 83 GLN cc_start: 0.7555 (pt0) cc_final: 0.7288 (pt0) REVERT: A 96 VAL cc_start: 0.6315 (OUTLIER) cc_final: 0.5994 (m) REVERT: A 122 GLN cc_start: 0.4423 (OUTLIER) cc_final: 0.4202 (mp10) REVERT: A 189 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6651 (tm-30) REVERT: A 252 TRP cc_start: 0.6764 (OUTLIER) cc_final: 0.5040 (m-90) REVERT: A 255 LYS cc_start: 0.6093 (mttt) cc_final: 0.5843 (mttp) REVERT: A 281 LYS cc_start: 0.5694 (mttm) cc_final: 0.4551 (mttt) outliers start: 55 outliers final: 32 residues processed: 205 average time/residue: 0.8897 time to fit residues: 197.0861 Evaluate side-chains 200 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 126 ASN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.248994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.237120 restraints weight = 9724.146| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 1.82 r_work: 0.4673 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4584 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 8319 Z= 0.456 Angle : 0.876 10.369 11265 Z= 0.469 Chirality : 0.053 0.202 1128 Planarity : 0.006 0.064 1530 Dihedral : 5.929 23.152 1164 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 8.73 % Allowed : 27.03 % Favored : 64.24 % 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: -2.50 (0.24), residues: 1032 helix: -1.90 (0.75), residues: 42 sheet: -0.54 (0.22), residues: 540 loop : -3.11 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 252 HIS 0.004 0.002 HIS A 21 PHE 0.022 0.003 PHE A 120 TYR 0.027 0.003 TYR A 227 ARG 0.007 0.001 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 167 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: B 178 ASP cc_start: 0.6959 (m-30) cc_final: 0.6758 (m-30) REVERT: B 189 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6596 (tm-30) REVERT: B 281 LYS cc_start: 0.5403 (mttm) cc_final: 0.4316 (mptt) REVERT: C 27 LYS cc_start: 0.7610 (mptt) cc_final: 0.6869 (mmtp) REVERT: C 57 GLU cc_start: 0.7940 (tt0) cc_final: 0.7626 (tt0) REVERT: C 73 THR cc_start: 0.7543 (t) cc_final: 0.7252 (m) REVERT: C 120 PHE cc_start: 0.6465 (m-80) cc_final: 0.5922 (m-80) REVERT: C 126 ASN cc_start: 0.7287 (m110) cc_final: 0.7049 (m-40) REVERT: C 170 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5337 (ptp-170) REVERT: C 189 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6790 (tm-30) REVERT: C 219 GLU cc_start: 0.4855 (OUTLIER) cc_final: 0.3824 (mp0) REVERT: C 252 TRP cc_start: 0.6744 (OUTLIER) cc_final: 0.5613 (m-90) REVERT: C 258 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7059 (m110) REVERT: C 281 LYS cc_start: 0.5659 (mttm) cc_final: 0.4727 (mtmm) REVERT: C 294 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6470 (mm) REVERT: A 12 ASP cc_start: 0.6324 (p0) cc_final: 0.5980 (p0) REVERT: A 189 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6561 (tm-30) REVERT: A 217 ARG cc_start: 0.5648 (mtp85) cc_final: 0.5420 (mtp85) REVERT: A 219 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.3968 (mp0) REVERT: A 252 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.5209 (m-90) REVERT: A 255 LYS cc_start: 0.6082 (mttt) cc_final: 0.5792 (mttp) REVERT: A 281 LYS cc_start: 0.5732 (mttm) cc_final: 0.4578 (mttt) outliers start: 72 outliers final: 47 residues processed: 217 average time/residue: 0.8761 time to fit residues: 205.5085 Evaluate side-chains 214 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 83 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.259104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.247620 restraints weight = 9659.079| |-----------------------------------------------------------------------------| r_work (start): 0.4790 rms_B_bonded: 1.80 r_work: 0.4743 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4655 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8319 Z= 0.191 Angle : 0.681 9.241 11265 Z= 0.361 Chirality : 0.047 0.159 1128 Planarity : 0.004 0.059 1530 Dihedral : 5.010 19.322 1164 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.33 % Allowed : 31.64 % Favored : 63.03 % 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: -2.07 (0.24), residues: 1032 helix: -1.85 (0.71), residues: 42 sheet: -0.34 (0.21), residues: 546 loop : -2.70 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 56 HIS 0.001 0.001 HIS A 21 PHE 0.017 0.001 PHE A 269 TYR 0.027 0.002 TYR A 98 ARG 0.008 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.834 Fit side-chains REVERT: B 69 ASN cc_start: 0.6774 (t0) cc_final: 0.6353 (t0) REVERT: B 189 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6867 (tm-30) REVERT: B 281 LYS cc_start: 0.5079 (mttm) cc_final: 0.4025 (mttt) REVERT: B 319 ASN cc_start: 0.6766 (t0) cc_final: 0.6361 (t0) REVERT: C 27 LYS cc_start: 0.7552 (mptt) cc_final: 0.6804 (mmtp) REVERT: C 51 THR cc_start: 0.6067 (OUTLIER) cc_final: 0.5855 (m) REVERT: C 120 PHE cc_start: 0.6206 (m-80) cc_final: 0.5861 (m-80) REVERT: C 126 ASN cc_start: 0.7171 (m110) cc_final: 0.6941 (m-40) REVERT: C 170 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5299 (pmm-80) REVERT: C 189 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6671 (tm-30) REVERT: C 219 GLU cc_start: 0.4755 (OUTLIER) cc_final: 0.3674 (mp0) REVERT: C 281 LYS cc_start: 0.5539 (mttm) cc_final: 0.4366 (mptt) REVERT: A 12 ASP cc_start: 0.5980 (p0) cc_final: 0.5630 (p0) REVERT: A 73 THR cc_start: 0.7174 (t) cc_final: 0.6961 (p) REVERT: A 92 ARG cc_start: 0.6092 (ttt180) cc_final: 0.5861 (tpt170) REVERT: A 189 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6586 (tm-30) REVERT: A 255 LYS cc_start: 0.5980 (mttt) cc_final: 0.5654 (mttp) REVERT: A 281 LYS cc_start: 0.5669 (mttm) cc_final: 0.4574 (mttt) REVERT: A 291 ASP cc_start: 0.6489 (m-30) cc_final: 0.6251 (t0) outliers start: 44 outliers final: 28 residues processed: 200 average time/residue: 0.8681 time to fit residues: 188.1775 Evaluate side-chains 186 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.248734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.237012 restraints weight = 9879.353| |-----------------------------------------------------------------------------| r_work (start): 0.4720 rms_B_bonded: 1.82 r_work: 0.4674 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4584 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 8319 Z= 0.486 Angle : 0.924 10.376 11265 Z= 0.494 Chirality : 0.055 0.242 1128 Planarity : 0.006 0.058 1530 Dihedral : 5.960 23.639 1164 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 7.64 % Allowed : 29.94 % Favored : 62.42 % 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: -2.41 (0.24), residues: 1032 helix: -1.98 (0.71), residues: 42 sheet: -0.48 (0.22), residues: 543 loop : -3.05 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 252 HIS 0.004 0.002 HIS A 21 PHE 0.029 0.003 PHE B 40 TYR 0.035 0.004 TYR A 98 ARG 0.008 0.001 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: B 174 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5013 (mtp180) REVERT: B 189 GLU cc_start: 0.7472 (tm-30) cc_final: 0.6653 (tm-30) REVERT: B 281 LYS cc_start: 0.5422 (mttm) cc_final: 0.4342 (mptt) REVERT: C 27 LYS cc_start: 0.7620 (mptt) cc_final: 0.6883 (mmtp) REVERT: C 49 GLN cc_start: 0.6982 (mt0) cc_final: 0.6740 (mm-40) REVERT: C 73 THR cc_start: 0.7488 (t) cc_final: 0.7154 (m) REVERT: C 126 ASN cc_start: 0.7246 (m110) cc_final: 0.7018 (m-40) REVERT: C 170 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.5374 (ptp-170) REVERT: C 178 ASP cc_start: 0.7208 (m-30) cc_final: 0.6822 (m-30) REVERT: C 189 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 219 GLU cc_start: 0.4880 (OUTLIER) cc_final: 0.3843 (mp0) REVERT: C 281 LYS cc_start: 0.5549 (mttm) cc_final: 0.4681 (mtmm) REVERT: A 12 ASP cc_start: 0.6327 (p0) cc_final: 0.6002 (p0) REVERT: A 57 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: A 189 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6559 (tm-30) REVERT: A 217 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5317 (mtp85) REVERT: A 252 TRP cc_start: 0.7001 (OUTLIER) cc_final: 0.5445 (m-90) REVERT: A 255 LYS cc_start: 0.6061 (mttt) cc_final: 0.5782 (mttp) REVERT: A 281 LYS cc_start: 0.5652 (mttm) cc_final: 0.4719 (mttp) outliers start: 63 outliers final: 37 residues processed: 210 average time/residue: 0.8634 time to fit residues: 197.0262 Evaluate side-chains 202 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 69 ASN C 83 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.257527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.245819 restraints weight = 9605.327| |-----------------------------------------------------------------------------| r_work (start): 0.4790 rms_B_bonded: 1.81 r_work: 0.4745 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4656 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8319 Z= 0.202 Angle : 0.717 9.382 11265 Z= 0.379 Chirality : 0.047 0.144 1128 Planarity : 0.004 0.060 1530 Dihedral : 5.165 20.869 1164 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.48 % Allowed : 32.97 % Favored : 62.55 % 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: -2.09 (0.25), residues: 1032 helix: -1.88 (0.73), residues: 42 sheet: -0.34 (0.21), residues: 546 loop : -2.73 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 56 HIS 0.002 0.001 HIS A 21 PHE 0.033 0.002 PHE B 40 TYR 0.029 0.002 TYR B 98 ARG 0.003 0.000 ARG B 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.823 Fit side-chains REVERT: B 69 ASN cc_start: 0.6740 (t0) cc_final: 0.6234 (t0) REVERT: B 189 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6816 (tm-30) REVERT: B 281 LYS cc_start: 0.5126 (mttm) cc_final: 0.4069 (mptt) REVERT: B 319 ASN cc_start: 0.6869 (t0) cc_final: 0.6457 (t0) REVERT: C 27 LYS cc_start: 0.7575 (mptt) cc_final: 0.6603 (mmtt) REVERT: C 48 ASP cc_start: 0.7697 (t0) cc_final: 0.7447 (t0) REVERT: C 126 ASN cc_start: 0.7154 (m110) cc_final: 0.6903 (m-40) REVERT: C 170 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.5325 (pmm-80) REVERT: C 189 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6741 (tm-30) REVERT: C 219 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.3647 (mp0) REVERT: C 281 LYS cc_start: 0.5354 (mttm) cc_final: 0.4210 (mptt) REVERT: A 12 ASP cc_start: 0.5957 (p0) cc_final: 0.5627 (p0) REVERT: A 96 VAL cc_start: 0.6402 (OUTLIER) cc_final: 0.6076 (m) REVERT: A 189 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 252 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.5072 (m-90) REVERT: A 255 LYS cc_start: 0.5942 (mttt) cc_final: 0.5619 (mttp) REVERT: A 281 LYS cc_start: 0.5684 (mttm) cc_final: 0.4574 (mttt) REVERT: A 291 ASP cc_start: 0.6421 (m-30) cc_final: 0.6154 (t0) outliers start: 37 outliers final: 25 residues processed: 190 average time/residue: 0.8624 time to fit residues: 177.6608 Evaluate side-chains 185 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.254237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.242673 restraints weight = 9797.787| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 1.79 r_work: 0.4714 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4625 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8319 Z= 0.291 Angle : 0.782 9.803 11265 Z= 0.415 Chirality : 0.048 0.157 1128 Planarity : 0.004 0.057 1530 Dihedral : 5.378 21.971 1164 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.06 % Allowed : 31.52 % Favored : 62.42 % 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: -2.09 (0.25), residues: 1032 helix: -1.72 (0.76), residues: 42 sheet: -0.37 (0.21), residues: 549 loop : -2.72 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 252 HIS 0.003 0.001 HIS A 21 PHE 0.036 0.002 PHE B 40 TYR 0.033 0.003 TYR B 98 ARG 0.007 0.001 ARG C 217 =============================================================================== Job complete usr+sys time: 5661.49 seconds wall clock time: 100 minutes 47.75 seconds (6047.75 seconds total)