Starting phenix.real_space_refine on Fri Sep 27 12:30:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/09_2024/7cr4_30447_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/09_2024/7cr4_30447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/09_2024/7cr4_30447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/09_2024/7cr4_30447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/09_2024/7cr4_30447_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/09_2024/7cr4_30447_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians S 88 5.16 5 Cl 4 4.86 5 C 10288 2.51 5 N 2724 2.21 5 O 2880 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15988 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "C" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1125 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, F, E, G, H Time building chain proxies: 7.13, per 1000 atoms: 0.45 Number of scatterers: 15988 At special positions: 0 Unit cell: (126.75, 126.75, 119.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 88 16.00 F 4 9.00 O 2880 8.00 N 2724 7.00 C 10288 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 80.5% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 114 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.778A pdb=" N TYR A 118 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.505A pdb=" N CYS A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 166 through 182 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.595A pdb=" N LYS A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.568A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 329 removed outlier: 3.892A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 536 through 559 Processing helix chain 'A' and resid 562 through 594 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 148 Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 90 through 114 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.778A pdb=" N TYR B 118 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 147 Processing helix chain 'B' and resid 148 through 151 removed outlier: 3.504A pdb=" N CYS B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 166 through 182 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.596A pdb=" N LYS B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.568A pdb=" N ALA B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 329 removed outlier: 3.891A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 536 through 559 Processing helix chain 'B' and resid 562 through 594 Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 90 through 114 Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.777A pdb=" N TYR D 118 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 147 Processing helix chain 'D' and resid 148 through 151 removed outlier: 3.504A pdb=" N CYS D 151 " --> pdb=" O ALA D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 151' Processing helix chain 'D' and resid 157 through 165 Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 215 through 228 removed outlier: 3.595A pdb=" N LYS D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.567A pdb=" N ALA D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.891A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 536 through 559 Processing helix chain 'D' and resid 562 through 594 Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'F' and resid 71 through 86 Processing helix chain 'F' and resid 90 through 114 Processing helix chain 'F' and resid 115 through 119 removed outlier: 3.778A pdb=" N TYR F 118 " --> pdb=" O ILE F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 147 Processing helix chain 'F' and resid 148 through 151 removed outlier: 3.504A pdb=" N CYS F 151 " --> pdb=" O ALA F 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 148 through 151' Processing helix chain 'F' and resid 157 through 165 Processing helix chain 'F' and resid 166 through 182 Processing helix chain 'F' and resid 196 through 210 Processing helix chain 'F' and resid 215 through 228 removed outlier: 3.596A pdb=" N LYS F 219 " --> pdb=" O GLY F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 255 Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.568A pdb=" N ALA F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 329 removed outlier: 3.891A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 332 through 350 Processing helix chain 'F' and resid 357 through 366 Processing helix chain 'F' and resid 536 through 559 Processing helix chain 'F' and resid 562 through 594 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 103 through 111 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.670A pdb=" N ILE H 101 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.670A pdb=" N ILE C 101 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.669A pdb=" N ILE E 101 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 102 removed outlier: 3.669A pdb=" N ILE G 101 " --> pdb=" O VAL G 137 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3531 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: 4.61 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2592 1.30 - 1.43: 4474 1.43 - 1.56: 9106 1.56 - 1.68: 0 1.68 - 1.81: 152 Bond restraints: 16324 Sorted by residual: bond pdb=" C12 GB9 B1001 " pdb=" N2 GB9 B1001 " ideal model delta sigma weight residual 1.306 1.482 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C12 GB9 F1001 " pdb=" N2 GB9 F1001 " ideal model delta sigma weight residual 1.306 1.482 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C12 GB9 A1001 " pdb=" N2 GB9 A1001 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.70e+01 bond pdb=" C12 GB9 D1001 " pdb=" N2 GB9 D1001 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C5 GB9 A1001 " pdb=" C8 GB9 A1001 " ideal model delta sigma weight residual 1.386 1.529 -0.143 2.00e-02 2.50e+03 5.12e+01 ... (remaining 16319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 21580 1.90 - 3.80: 388 3.80 - 5.70: 28 5.70 - 7.60: 8 7.60 - 9.50: 8 Bond angle restraints: 22012 Sorted by residual: angle pdb=" CA LEU A 272 " pdb=" CB LEU A 272 " pdb=" CG LEU A 272 " ideal model delta sigma weight residual 116.30 106.80 9.50 3.50e+00 8.16e-02 7.37e+00 angle pdb=" CA LEU B 272 " pdb=" CB LEU B 272 " pdb=" CG LEU B 272 " ideal model delta sigma weight residual 116.30 106.83 9.47 3.50e+00 8.16e-02 7.32e+00 angle pdb=" CA LEU F 272 " pdb=" CB LEU F 272 " pdb=" CG LEU F 272 " ideal model delta sigma weight residual 116.30 106.83 9.47 3.50e+00 8.16e-02 7.32e+00 angle pdb=" CA LEU D 272 " pdb=" CB LEU D 272 " pdb=" CG LEU D 272 " ideal model delta sigma weight residual 116.30 106.89 9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" C2 GB9 D1001 " pdb=" N1 GB9 D1001 " pdb=" C3 GB9 D1001 " ideal model delta sigma weight residual 128.33 120.50 7.83 3.00e+00 1.11e-01 6.81e+00 ... (remaining 22007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8659 17.86 - 35.71: 849 35.71 - 53.57: 68 53.57 - 71.42: 12 71.42 - 89.28: 8 Dihedral angle restraints: 9596 sinusoidal: 3900 harmonic: 5696 Sorted by residual: dihedral pdb=" CA SER D 122 " pdb=" C SER D 122 " pdb=" N GLU D 123 " pdb=" CA GLU D 123 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER F 122 " pdb=" C SER F 122 " pdb=" N GLU F 123 " pdb=" CA GLU F 123 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER B 122 " pdb=" C SER B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1368 0.025 - 0.049: 621 0.049 - 0.074: 304 0.074 - 0.098: 83 0.098 - 0.123: 28 Chirality restraints: 2404 Sorted by residual: chirality pdb=" CA PRO F 308 " pdb=" N PRO F 308 " pdb=" C PRO F 308 " pdb=" CB PRO F 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA PRO B 308 " pdb=" N PRO B 308 " pdb=" C PRO B 308 " pdb=" CB PRO B 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 2401 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 166 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.64e-01 pdb=" N PRO F 167 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 166 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.64e-01 pdb=" N PRO B 167 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 166 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.62e-01 pdb=" N PRO D 167 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " 0.014 5.00e-02 4.00e+02 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 197 2.45 - 3.06: 14779 3.06 - 3.67: 28405 3.67 - 4.29: 41579 4.29 - 4.90: 59909 Nonbonded interactions: 144869 Sorted by model distance: nonbonded pdb=" OH TYR B 571 " pdb=" O VAL F 567 " model vdw 1.833 3.040 nonbonded pdb=" NE2 GLN F 341 " pdb=" O MET G 110 " model vdw 1.905 3.120 nonbonded pdb=" OG SER A 179 " pdb=" F1 GB9 A1001 " model vdw 1.973 2.990 nonbonded pdb=" OG SER B 179 " pdb=" F1 GB9 B1001 " model vdw 1.973 2.990 nonbonded pdb=" OG SER F 179 " pdb=" F1 GB9 F1001 " model vdw 1.973 2.990 ... (remaining 144864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 33.190 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.008 0.176 16324 Z= 0.479 Angle : 0.650 9.501 22012 Z= 0.384 Chirality : 0.036 0.123 2404 Planarity : 0.003 0.025 2780 Dihedral : 13.143 89.277 5932 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 102.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.16), residues: 1936 helix: -1.78 (0.11), residues: 1484 sheet: None (None), residues: 0 loop : -1.63 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.007 0.002 HIS B 328 PHE 0.012 0.002 PHE A 261 TYR 0.013 0.002 TYR D 571 ARG 0.004 0.000 ARG D 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.9236 (tt0) cc_final: 0.8761 (tp30) REVERT: A 210 ARG cc_start: 0.9215 (ttt90) cc_final: 0.8339 (ttt90) REVERT: A 553 ARG cc_start: 0.9026 (mmp-170) cc_final: 0.8665 (mmp-170) REVERT: B 130 GLU cc_start: 0.9210 (tt0) cc_final: 0.8646 (tp30) REVERT: B 174 MET cc_start: 0.8611 (ttt) cc_final: 0.8367 (tmm) REVERT: B 293 LEU cc_start: 0.9483 (pp) cc_final: 0.9272 (pp) REVERT: B 565 MET cc_start: 0.7017 (mtm) cc_final: 0.6605 (ttt) REVERT: B 569 GLU cc_start: 0.9040 (pt0) cc_final: 0.8705 (mp0) REVERT: D 172 ASP cc_start: 0.9075 (t70) cc_final: 0.8650 (t70) REVERT: D 219 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8234 (mmtm) REVERT: D 341 GLN cc_start: 0.8601 (mt0) cc_final: 0.8323 (mt0) REVERT: D 565 MET cc_start: 0.7209 (mtm) cc_final: 0.6916 (ttt) REVERT: F 130 GLU cc_start: 0.9206 (tt0) cc_final: 0.8635 (tp30) REVERT: F 174 MET cc_start: 0.8631 (ttt) cc_final: 0.8385 (tmm) REVERT: F 565 MET cc_start: 0.7010 (mtm) cc_final: 0.6596 (ttt) REVERT: F 569 GLU cc_start: 0.9055 (pt0) cc_final: 0.8696 (mp0) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.2923 time to fit residues: 163.3411 Evaluate side-chains 286 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16324 Z= 0.304 Angle : 0.707 11.985 22012 Z= 0.380 Chirality : 0.043 0.173 2404 Planarity : 0.005 0.046 2780 Dihedral : 4.761 22.677 2180 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 13.39 % Favored : 83.04 % 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: -0.89 (0.17), residues: 1936 helix: -0.26 (0.12), residues: 1564 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 344 HIS 0.008 0.001 HIS B 324 PHE 0.018 0.002 PHE A 297 TYR 0.020 0.002 TYR B 571 ARG 0.007 0.001 ARG F 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 363 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASN cc_start: 0.9514 (t0) cc_final: 0.9105 (p0) REVERT: A 319 LYS cc_start: 0.8987 (tttt) cc_final: 0.8680 (tmtt) REVERT: B 83 ASN cc_start: 0.9530 (t0) cc_final: 0.9144 (p0) REVERT: B 174 MET cc_start: 0.8639 (ttt) cc_final: 0.8334 (tmm) REVERT: B 293 LEU cc_start: 0.9374 (pp) cc_final: 0.9034 (pp) REVERT: B 570 GLN cc_start: 0.8047 (tt0) cc_final: 0.7793 (tt0) REVERT: D 83 ASN cc_start: 0.9512 (t0) cc_final: 0.9131 (p0) REVERT: D 172 ASP cc_start: 0.8875 (t70) cc_final: 0.8544 (t0) REVERT: D 322 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: E 86 ILE cc_start: 0.7919 (tt) cc_final: 0.7642 (tt) REVERT: E 146 MET cc_start: 0.8447 (mtm) cc_final: 0.8063 (ptm) REVERT: F 83 ASN cc_start: 0.9539 (t0) cc_final: 0.9160 (p0) REVERT: F 174 MET cc_start: 0.8659 (ttt) cc_final: 0.8351 (tmm) REVERT: F 293 LEU cc_start: 0.9410 (pp) cc_final: 0.9083 (pp) REVERT: F 319 LYS cc_start: 0.9024 (tttt) cc_final: 0.8644 (tmtt) REVERT: F 322 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: F 323 GLN cc_start: 0.9062 (tp40) cc_final: 0.8658 (tp40) REVERT: G 86 ILE cc_start: 0.8008 (tt) cc_final: 0.7766 (tt) REVERT: G 146 MET cc_start: 0.8563 (mtm) cc_final: 0.7978 (ptm) outliers start: 60 outliers final: 32 residues processed: 385 average time/residue: 0.2742 time to fit residues: 154.2837 Evaluate side-chains 340 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 306 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 30.0000 chunk 174 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 HIS ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16324 Z= 0.352 Angle : 0.682 9.569 22012 Z= 0.373 Chirality : 0.042 0.231 2404 Planarity : 0.004 0.038 2780 Dihedral : 4.725 25.464 2180 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.70 % Allowed : 16.37 % Favored : 78.93 % 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: -0.34 (0.18), residues: 1936 helix: 0.09 (0.12), residues: 1564 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 288 HIS 0.006 0.001 HIS B 328 PHE 0.019 0.002 PHE F 297 TYR 0.017 0.002 TYR G 139 ARG 0.006 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 328 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: A 293 LEU cc_start: 0.9366 (pp) cc_final: 0.9144 (pp) REVERT: H 101 ILE cc_start: 0.5133 (OUTLIER) cc_final: 0.4335 (mm) REVERT: B 174 MET cc_start: 0.8630 (ttt) cc_final: 0.8344 (tmm) REVERT: B 293 LEU cc_start: 0.9327 (pp) cc_final: 0.9019 (pp) REVERT: B 570 GLN cc_start: 0.8148 (tt0) cc_final: 0.7881 (tt0) REVERT: C 145 MET cc_start: 0.3937 (ppp) cc_final: 0.3660 (ppp) REVERT: C 146 MET cc_start: 0.9000 (mtm) cc_final: 0.8439 (ptm) REVERT: D 172 ASP cc_start: 0.8808 (t70) cc_final: 0.8462 (t70) REVERT: D 174 MET cc_start: 0.8615 (ttt) cc_final: 0.8406 (tmm) REVERT: E 72 MET cc_start: 0.5227 (ptt) cc_final: 0.4874 (ptt) REVERT: E 73 MET cc_start: 0.1950 (tpt) cc_final: 0.1273 (ptt) REVERT: E 101 ILE cc_start: 0.4766 (OUTLIER) cc_final: 0.4126 (mm) REVERT: F 174 MET cc_start: 0.8653 (ttt) cc_final: 0.8381 (tmm) REVERT: F 273 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9113 (tp) REVERT: F 293 LEU cc_start: 0.9370 (pp) cc_final: 0.9081 (pp) REVERT: F 322 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: G 46 GLU cc_start: 0.8183 (pp20) cc_final: 0.7933 (mm-30) REVERT: G 52 MET cc_start: 0.0518 (mmt) cc_final: 0.0269 (mmp) REVERT: G 101 ILE cc_start: 0.4573 (OUTLIER) cc_final: 0.3986 (mm) outliers start: 79 outliers final: 52 residues processed: 372 average time/residue: 0.2718 time to fit residues: 148.8972 Evaluate side-chains 359 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 301 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16324 Z= 0.248 Angle : 0.634 8.568 22012 Z= 0.342 Chirality : 0.041 0.235 2404 Planarity : 0.004 0.050 2780 Dihedral : 4.539 27.651 2180 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.94 % Allowed : 18.27 % Favored : 76.79 % 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: 0.25 (0.19), residues: 1936 helix: 0.52 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 288 HIS 0.003 0.001 HIS B 328 PHE 0.022 0.002 PHE C 90 TYR 0.015 0.002 TYR H 139 ARG 0.010 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 352 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9333 (mm) cc_final: 0.9124 (pp) REVERT: A 174 MET cc_start: 0.8685 (ttt) cc_final: 0.8441 (tmm) REVERT: A 202 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: A 293 LEU cc_start: 0.9254 (pp) cc_final: 0.9036 (pp) REVERT: H 52 MET cc_start: 0.0680 (mmt) cc_final: 0.0292 (mmp) REVERT: H 101 ILE cc_start: 0.4702 (OUTLIER) cc_final: 0.4087 (mm) REVERT: B 174 MET cc_start: 0.8659 (ttt) cc_final: 0.8297 (tmm) REVERT: B 293 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8972 (pp) REVERT: B 570 GLN cc_start: 0.8195 (tt0) cc_final: 0.7904 (tt0) REVERT: C 52 MET cc_start: 0.0461 (mmt) cc_final: 0.0178 (mmt) REVERT: C 101 ILE cc_start: 0.4830 (OUTLIER) cc_final: 0.4215 (mm) REVERT: C 146 MET cc_start: 0.9043 (mtm) cc_final: 0.8385 (ptm) REVERT: D 172 ASP cc_start: 0.8795 (t70) cc_final: 0.8390 (t0) REVERT: D 174 MET cc_start: 0.8614 (ttt) cc_final: 0.8362 (tmm) REVERT: D 322 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: D 570 GLN cc_start: 0.8590 (tt0) cc_final: 0.7654 (tt0) REVERT: E 72 MET cc_start: 0.5182 (ptt) cc_final: 0.4566 (ptt) REVERT: E 73 MET cc_start: 0.1903 (tpt) cc_final: 0.1417 (ptt) REVERT: E 125 MET cc_start: 0.7951 (mtt) cc_final: 0.7566 (tpp) REVERT: F 174 MET cc_start: 0.8691 (ttt) cc_final: 0.8317 (tmm) REVERT: F 293 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9038 (pp) REVERT: G 46 GLU cc_start: 0.8155 (pp20) cc_final: 0.7829 (mm-30) REVERT: G 52 MET cc_start: 0.0744 (mmt) cc_final: 0.0538 (mmp) outliers start: 83 outliers final: 55 residues processed: 387 average time/residue: 0.2749 time to fit residues: 156.4782 Evaluate side-chains 378 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 317 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 108 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 166 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 HIS E 42 GLN E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16324 Z= 0.248 Angle : 0.647 8.455 22012 Z= 0.348 Chirality : 0.041 0.191 2404 Planarity : 0.004 0.037 2780 Dihedral : 4.478 27.375 2180 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.42 % Allowed : 20.95 % Favored : 73.63 % 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: 0.51 (0.19), residues: 1936 helix: 0.73 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.91 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 288 HIS 0.005 0.001 HIS A 575 PHE 0.022 0.002 PHE C 90 TYR 0.016 0.002 TYR D 571 ARG 0.007 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 339 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9351 (mm) cc_final: 0.9141 (pp) REVERT: A 174 MET cc_start: 0.8638 (ttt) cc_final: 0.8427 (tmm) REVERT: A 202 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: A 293 LEU cc_start: 0.9256 (pp) cc_final: 0.8980 (pp) REVERT: A 327 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8202 (pttt) REVERT: A 570 GLN cc_start: 0.8377 (tt0) cc_final: 0.7648 (tt0) REVERT: H 52 MET cc_start: 0.0780 (mmt) cc_final: 0.0388 (mmp) REVERT: H 101 ILE cc_start: 0.4441 (OUTLIER) cc_final: 0.4170 (mp) REVERT: B 174 MET cc_start: 0.8679 (ttt) cc_final: 0.8276 (tmm) REVERT: B 293 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8979 (pp) REVERT: B 565 MET cc_start: 0.7731 (mmt) cc_final: 0.7461 (mmt) REVERT: C 37 MET cc_start: 0.8622 (tmm) cc_final: 0.8397 (tmm) REVERT: C 52 MET cc_start: 0.0616 (mmt) cc_final: 0.0212 (mmt) REVERT: C 101 ILE cc_start: 0.4671 (OUTLIER) cc_final: 0.4125 (mm) REVERT: C 145 MET cc_start: 0.3103 (ppp) cc_final: 0.2826 (ppp) REVERT: C 146 MET cc_start: 0.8961 (mtm) cc_final: 0.8501 (ptm) REVERT: D 172 ASP cc_start: 0.8772 (t70) cc_final: 0.8444 (t0) REVERT: D 174 MET cc_start: 0.8647 (ttt) cc_final: 0.8371 (tmm) REVERT: D 322 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: D 565 MET cc_start: 0.7752 (mpp) cc_final: 0.7533 (mmp) REVERT: E 72 MET cc_start: 0.5165 (ptt) cc_final: 0.4541 (ptt) REVERT: E 73 MET cc_start: 0.2051 (tpt) cc_final: 0.1637 (ptt) REVERT: F 174 MET cc_start: 0.8717 (ttt) cc_final: 0.8323 (tmm) REVERT: F 266 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7228 (t70) REVERT: F 293 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9020 (pp) REVERT: F 565 MET cc_start: 0.7697 (mmt) cc_final: 0.7443 (mmm) REVERT: G 46 GLU cc_start: 0.8200 (pp20) cc_final: 0.7925 (mm-30) REVERT: G 52 MET cc_start: 0.0979 (mmt) cc_final: 0.0720 (mmp) outliers start: 91 outliers final: 58 residues processed: 383 average time/residue: 0.2655 time to fit residues: 150.3458 Evaluate side-chains 374 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 308 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS D 341 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16324 Z= 0.228 Angle : 0.689 11.530 22012 Z= 0.360 Chirality : 0.042 0.234 2404 Planarity : 0.004 0.040 2780 Dihedral : 4.476 27.532 2180 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.52 % Allowed : 23.27 % Favored : 72.20 % 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: 0.76 (0.19), residues: 1936 helix: 0.84 (0.13), residues: 1564 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.006 0.001 HIS A 328 PHE 0.024 0.002 PHE B 555 TYR 0.018 0.002 TYR A 347 ARG 0.010 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 342 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8648 (ttt) cc_final: 0.8418 (tmm) REVERT: A 293 LEU cc_start: 0.9122 (pp) cc_final: 0.8891 (pp) REVERT: A 583 LYS cc_start: 0.9625 (mmtt) cc_final: 0.9268 (tptt) REVERT: H 52 MET cc_start: 0.0613 (mmt) cc_final: 0.0274 (mmp) REVERT: H 101 ILE cc_start: 0.4123 (OUTLIER) cc_final: 0.3797 (mp) REVERT: B 172 ASP cc_start: 0.8785 (t70) cc_final: 0.8520 (t0) REVERT: B 174 MET cc_start: 0.8677 (ttt) cc_final: 0.8274 (tmm) REVERT: B 293 LEU cc_start: 0.9138 (pp) cc_final: 0.8871 (pp) REVERT: B 565 MET cc_start: 0.7617 (mmt) cc_final: 0.7406 (mmt) REVERT: C 52 MET cc_start: 0.0610 (mmt) cc_final: 0.0280 (mmt) REVERT: C 101 ILE cc_start: 0.4435 (OUTLIER) cc_final: 0.3794 (mm) REVERT: C 146 MET cc_start: 0.8973 (mtm) cc_final: 0.8376 (ptm) REVERT: D 174 MET cc_start: 0.8680 (ttt) cc_final: 0.8326 (tmm) REVERT: D 565 MET cc_start: 0.7730 (mpp) cc_final: 0.7414 (mmt) REVERT: E 72 MET cc_start: 0.5398 (ptt) cc_final: 0.4775 (ptt) REVERT: E 73 MET cc_start: 0.2020 (tpt) cc_final: 0.1641 (ptt) REVERT: E 101 ILE cc_start: 0.4745 (OUTLIER) cc_final: 0.4123 (mm) REVERT: E 125 MET cc_start: 0.7921 (mtt) cc_final: 0.7413 (tpp) REVERT: F 174 MET cc_start: 0.8708 (ttt) cc_final: 0.8292 (tmm) REVERT: F 266 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7287 (t70) REVERT: F 293 LEU cc_start: 0.9169 (pp) cc_final: 0.8922 (pp) REVERT: G 46 GLU cc_start: 0.8064 (pp20) cc_final: 0.7830 (mm-30) REVERT: G 52 MET cc_start: 0.1025 (mmt) cc_final: 0.0765 (mmp) REVERT: G 101 ILE cc_start: 0.4756 (OUTLIER) cc_final: 0.4450 (mp) outliers start: 76 outliers final: 61 residues processed: 378 average time/residue: 0.2637 time to fit residues: 148.2891 Evaluate side-chains 384 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 318 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 40.0000 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16324 Z= 0.250 Angle : 0.717 12.767 22012 Z= 0.377 Chirality : 0.043 0.215 2404 Planarity : 0.004 0.048 2780 Dihedral : 4.544 32.027 2180 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.52 % Allowed : 24.40 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1936 helix: 0.83 (0.13), residues: 1564 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.008 0.001 HIS A 328 PHE 0.026 0.002 PHE D 548 TYR 0.023 0.002 TYR F 347 ARG 0.006 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 324 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8634 (ttt) cc_final: 0.8432 (tmm) REVERT: A 293 LEU cc_start: 0.9180 (pp) cc_final: 0.8921 (pp) REVERT: H 52 MET cc_start: 0.0502 (mmt) cc_final: 0.0184 (mmp) REVERT: H 101 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3075 (mp) REVERT: B 172 ASP cc_start: 0.8836 (t70) cc_final: 0.8581 (t0) REVERT: B 293 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8900 (pp) REVERT: B 565 MET cc_start: 0.7648 (mmt) cc_final: 0.7260 (mmt) REVERT: C 52 MET cc_start: 0.0671 (mmt) cc_final: 0.0269 (mmt) REVERT: C 72 MET cc_start: 0.4318 (ptt) cc_final: 0.3848 (ptt) REVERT: C 82 SER cc_start: 0.7697 (p) cc_final: 0.7266 (t) REVERT: C 101 ILE cc_start: 0.4682 (OUTLIER) cc_final: 0.4017 (mm) REVERT: C 146 MET cc_start: 0.8914 (mtm) cc_final: 0.8476 (ptm) REVERT: D 174 MET cc_start: 0.8680 (ttt) cc_final: 0.8318 (tmm) REVERT: D 565 MET cc_start: 0.7650 (mpp) cc_final: 0.7263 (mmm) REVERT: D 570 GLN cc_start: 0.8659 (tt0) cc_final: 0.8393 (tt0) REVERT: E 72 MET cc_start: 0.5561 (ptt) cc_final: 0.5092 (ptm) REVERT: E 73 MET cc_start: 0.2216 (tpt) cc_final: 0.1798 (ptt) REVERT: E 101 ILE cc_start: 0.4625 (OUTLIER) cc_final: 0.3936 (mm) REVERT: E 125 MET cc_start: 0.7844 (mtt) cc_final: 0.7274 (tpt) REVERT: F 174 MET cc_start: 0.8696 (ttt) cc_final: 0.8307 (tmm) REVERT: F 266 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7311 (t70) REVERT: F 293 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8946 (pp) REVERT: G 52 MET cc_start: 0.1213 (mmt) cc_final: 0.0902 (mmp) REVERT: G 101 ILE cc_start: 0.4744 (OUTLIER) cc_final: 0.4047 (mm) outliers start: 76 outliers final: 56 residues processed: 362 average time/residue: 0.2577 time to fit residues: 138.7894 Evaluate side-chains 356 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 293 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 40.0000 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16324 Z= 0.232 Angle : 0.757 15.345 22012 Z= 0.391 Chirality : 0.043 0.193 2404 Planarity : 0.004 0.052 2780 Dihedral : 4.525 34.998 2180 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.11 % Allowed : 25.30 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 1936 helix: 0.92 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 344 HIS 0.004 0.001 HIS F 328 PHE 0.034 0.002 PHE D 548 TYR 0.025 0.002 TYR A 141 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 328 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8663 (ttt) cc_final: 0.8340 (tmm) REVERT: A 266 ASP cc_start: 0.7635 (m-30) cc_final: 0.7267 (t70) REVERT: A 293 LEU cc_start: 0.9145 (pp) cc_final: 0.8869 (pp) REVERT: A 341 GLN cc_start: 0.9157 (mt0) cc_final: 0.8744 (mt0) REVERT: H 52 MET cc_start: 0.0610 (mmt) cc_final: 0.0238 (mmp) REVERT: H 73 MET cc_start: 0.2063 (tpt) cc_final: 0.1568 (ptt) REVERT: H 91 ARG cc_start: 0.8870 (mtm-85) cc_final: 0.8554 (mmt-90) REVERT: H 101 ILE cc_start: 0.3517 (OUTLIER) cc_final: 0.2967 (mp) REVERT: B 172 ASP cc_start: 0.8863 (t70) cc_final: 0.8547 (t0) REVERT: B 293 LEU cc_start: 0.9139 (pp) cc_final: 0.8870 (pp) REVERT: B 565 MET cc_start: 0.7581 (mmt) cc_final: 0.7251 (mmt) REVERT: C 52 MET cc_start: 0.0770 (mmt) cc_final: 0.0292 (mmt) REVERT: C 72 MET cc_start: 0.4350 (ptt) cc_final: 0.3946 (ptt) REVERT: C 82 SER cc_start: 0.7845 (p) cc_final: 0.7458 (t) REVERT: C 101 ILE cc_start: 0.4615 (OUTLIER) cc_final: 0.3972 (mm) REVERT: C 145 MET cc_start: 0.2844 (ppp) cc_final: 0.2548 (ppp) REVERT: C 146 MET cc_start: 0.8554 (mtm) cc_final: 0.7882 (ptm) REVERT: D 248 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7154 (t80) REVERT: D 323 GLN cc_start: 0.8784 (tp40) cc_final: 0.8378 (tp40) REVERT: D 570 GLN cc_start: 0.8714 (tt0) cc_final: 0.8421 (tt0) REVERT: D 585 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7901 (mt) REVERT: E 72 MET cc_start: 0.5629 (ptt) cc_final: 0.5067 (ptt) REVERT: E 73 MET cc_start: 0.2292 (tpt) cc_final: 0.1970 (ptt) REVERT: E 101 ILE cc_start: 0.4723 (OUTLIER) cc_final: 0.4297 (mm) REVERT: E 125 MET cc_start: 0.7698 (mtt) cc_final: 0.7095 (tpt) REVERT: F 266 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7316 (t70) REVERT: F 293 LEU cc_start: 0.9163 (pp) cc_final: 0.8906 (pp) REVERT: F 570 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8459 (tm-30) REVERT: G 52 MET cc_start: 0.1122 (mmt) cc_final: 0.0890 (mmp) REVERT: G 101 ILE cc_start: 0.4711 (OUTLIER) cc_final: 0.4226 (mm) outliers start: 69 outliers final: 54 residues processed: 363 average time/residue: 0.2789 time to fit residues: 150.9665 Evaluate side-chains 374 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 313 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 50.0000 chunk 135 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16324 Z= 0.315 Angle : 0.805 13.994 22012 Z= 0.422 Chirality : 0.045 0.236 2404 Planarity : 0.004 0.101 2780 Dihedral : 4.698 38.525 2180 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.11 % Allowed : 25.71 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1936 helix: 0.73 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 344 HIS 0.005 0.001 HIS F 328 PHE 0.040 0.002 PHE A 555 TYR 0.024 0.002 TYR F 347 ARG 0.007 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8641 (ttt) cc_final: 0.8426 (tmm) REVERT: A 266 ASP cc_start: 0.7791 (m-30) cc_final: 0.7480 (t70) REVERT: A 293 LEU cc_start: 0.9238 (pp) cc_final: 0.8948 (pp) REVERT: H 52 MET cc_start: 0.0821 (mmt) cc_final: 0.0517 (mmp) REVERT: H 73 MET cc_start: 0.2076 (tpt) cc_final: 0.1547 (ptt) REVERT: H 91 ARG cc_start: 0.8858 (mtm-85) cc_final: 0.8494 (mmt-90) REVERT: H 136 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8926 (tp40) REVERT: B 81 LEU cc_start: 0.9472 (mt) cc_final: 0.9268 (pp) REVERT: B 293 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8964 (pp) REVERT: B 565 MET cc_start: 0.7753 (mmt) cc_final: 0.7397 (mmt) REVERT: C 52 MET cc_start: 0.0712 (mmt) cc_final: 0.0199 (mmt) REVERT: C 72 MET cc_start: 0.4755 (ptt) cc_final: 0.4444 (ptt) REVERT: C 82 SER cc_start: 0.7866 (p) cc_final: 0.7438 (t) REVERT: C 101 ILE cc_start: 0.4426 (OUTLIER) cc_final: 0.4150 (mp) REVERT: C 145 MET cc_start: 0.3008 (ppp) cc_final: 0.2717 (ppp) REVERT: C 146 MET cc_start: 0.8532 (mtm) cc_final: 0.8010 (ptm) REVERT: D 81 LEU cc_start: 0.9413 (mt) cc_final: 0.9066 (pp) REVERT: D 248 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7244 (t80) REVERT: D 585 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8039 (mt) REVERT: E 72 MET cc_start: 0.5645 (ptt) cc_final: 0.5434 (ptm) REVERT: E 73 MET cc_start: 0.2343 (tpt) cc_final: 0.2050 (ptt) REVERT: E 101 ILE cc_start: 0.4380 (OUTLIER) cc_final: 0.3993 (mm) REVERT: E 125 MET cc_start: 0.7744 (mtt) cc_final: 0.7137 (tpt) REVERT: F 174 MET cc_start: 0.8732 (ttt) cc_final: 0.8332 (tmm) REVERT: F 266 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7298 (t70) REVERT: F 293 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9008 (pp) REVERT: F 570 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8705 (tm-30) REVERT: G 12 GLU cc_start: 0.0943 (OUTLIER) cc_final: 0.0625 (tm-30) REVERT: G 52 MET cc_start: 0.1238 (mmt) cc_final: 0.0882 (mmt) REVERT: G 101 ILE cc_start: 0.4765 (OUTLIER) cc_final: 0.4103 (mm) outliers start: 69 outliers final: 51 residues processed: 359 average time/residue: 0.2751 time to fit residues: 145.2537 Evaluate side-chains 364 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 304 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 126 optimal weight: 4.9990 chunk 191 optimal weight: 30.0000 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16324 Z= 0.263 Angle : 0.841 22.026 22012 Z= 0.431 Chirality : 0.045 0.276 2404 Planarity : 0.004 0.031 2780 Dihedral : 4.725 41.985 2180 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.27 % Allowed : 27.32 % Favored : 69.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1936 helix: 0.83 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 344 HIS 0.004 0.001 HIS F 328 PHE 0.036 0.002 PHE A 555 TYR 0.021 0.002 TYR A 237 ARG 0.006 0.000 ARG A 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 321 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8625 (ttt) cc_final: 0.8379 (tmm) REVERT: A 266 ASP cc_start: 0.7726 (m-30) cc_final: 0.7352 (t70) REVERT: A 293 LEU cc_start: 0.9165 (pp) cc_final: 0.8896 (pp) REVERT: A 583 LYS cc_start: 0.9593 (mmtt) cc_final: 0.9061 (tmtt) REVERT: H 52 MET cc_start: 0.0636 (mmt) cc_final: 0.0241 (mmt) REVERT: H 73 MET cc_start: 0.2110 (tpt) cc_final: 0.1634 (ptt) REVERT: H 91 ARG cc_start: 0.8867 (mtm-85) cc_final: 0.8641 (mpt180) REVERT: B 293 LEU cc_start: 0.9200 (pp) cc_final: 0.8927 (pp) REVERT: B 565 MET cc_start: 0.7761 (mmt) cc_final: 0.7420 (mmt) REVERT: C 52 MET cc_start: 0.0827 (mmt) cc_final: 0.0246 (mmt) REVERT: C 82 SER cc_start: 0.7939 (p) cc_final: 0.7504 (t) REVERT: C 101 ILE cc_start: 0.4404 (OUTLIER) cc_final: 0.4036 (mp) REVERT: C 145 MET cc_start: 0.2956 (ppp) cc_final: 0.2690 (ppp) REVERT: C 146 MET cc_start: 0.8569 (mtm) cc_final: 0.8012 (ptm) REVERT: D 81 LEU cc_start: 0.9408 (mt) cc_final: 0.9067 (pp) REVERT: D 248 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7195 (t80) REVERT: D 323 GLN cc_start: 0.8786 (tp40) cc_final: 0.8430 (tp40) REVERT: D 570 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8795 (tm-30) REVERT: D 585 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8279 (mt) REVERT: E 73 MET cc_start: 0.2244 (tpt) cc_final: 0.1980 (ptt) REVERT: E 101 ILE cc_start: 0.4515 (OUTLIER) cc_final: 0.4021 (mm) REVERT: E 125 MET cc_start: 0.7712 (mtt) cc_final: 0.7084 (tpt) REVERT: F 201 ARG cc_start: 0.8717 (mmt180) cc_final: 0.8511 (mmt180) REVERT: F 266 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7350 (t70) REVERT: F 293 LEU cc_start: 0.9226 (pp) cc_final: 0.8977 (pp) REVERT: F 570 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8720 (tm-30) REVERT: G 12 GLU cc_start: 0.1091 (OUTLIER) cc_final: 0.0758 (tm-30) REVERT: G 52 MET cc_start: 0.1290 (mmt) cc_final: 0.0963 (mmt) REVERT: G 101 ILE cc_start: 0.4678 (OUTLIER) cc_final: 0.4007 (mm) outliers start: 55 outliers final: 46 residues processed: 348 average time/residue: 0.2736 time to fit residues: 140.6206 Evaluate side-chains 364 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 311 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 HIS ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.128276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.083559 restraints weight = 61024.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085901 restraints weight = 29402.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.087073 restraints weight = 19209.829| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16324 Z= 0.219 Angle : 0.874 20.242 22012 Z= 0.435 Chirality : 0.045 0.237 2404 Planarity : 0.003 0.031 2780 Dihedral : 4.672 39.613 2180 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.80 % Allowed : 27.68 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1936 helix: 0.91 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.44 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 344 HIS 0.004 0.001 HIS D 328 PHE 0.034 0.002 PHE A 555 TYR 0.020 0.001 TYR A 237 ARG 0.006 0.000 ARG D 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3349.91 seconds wall clock time: 60 minutes 49.42 seconds (3649.42 seconds total)