Starting phenix.real_space_refine on Sat Mar 16 23:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/03_2024/7cr4_30447_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/03_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_30447/03_2024/7cr4_30447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/03_2024/7cr4_30447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/03_2024/7cr4_30447_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/03_2024/7cr4_30447_trim_updated.pdb" } 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 Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 144": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15988 Number of models: 1 Model: "" Number of chains: 12 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: "H" 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: "B" 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: "D" 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: "E" 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: "F" 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: "G" 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} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.83, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 8.00 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 90 helices and 4 sheets defined 74.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 114 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 123 through 148 Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.840A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 254 removed outlier: 5.493A pdb=" N LYS A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 328 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 333 through 349 Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 536 through 560 removed outlier: 4.220A pdb=" N ARG A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 593 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 73 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 123 through 148 Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.840A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 254 removed outlier: 5.493A pdb=" N LYS B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 328 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 333 through 349 Processing helix chain 'B' and resid 358 through 365 Processing helix chain 'B' and resid 536 through 560 removed outlier: 4.219A pdb=" N ARG B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 593 Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 123 through 148 Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.839A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 254 removed outlier: 5.492A pdb=" N LYS D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 328 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 333 through 349 Processing helix chain 'D' and resid 358 through 365 Processing helix chain 'D' and resid 536 through 560 removed outlier: 4.220A pdb=" N ARG D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 593 Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 91 through 114 Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 123 through 148 Processing helix chain 'F' and resid 158 through 164 Processing helix chain 'F' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.840A pdb=" N MET F 211 " --> pdb=" O ARG F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 254 removed outlier: 5.493A pdb=" N LYS F 230 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'F' and resid 288 through 328 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 333 through 349 Processing helix chain 'F' and resid 358 through 365 Processing helix chain 'F' and resid 536 through 560 removed outlier: 4.219A pdb=" N ARG F 560 " --> pdb=" O LYS F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 593 Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 66 through 73 Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 139 through 147 Processing sheet with id= A, 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= B, 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= C, 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= D, 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) 1068 hydrogen bonds defined for protein. 3204 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: 4.85 Time building geometry restraints manager: 8.38 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: 100.03 - 106.82: 264 106.82 - 113.60: 9068 113.60 - 120.39: 6523 120.39 - 127.18: 6017 127.18 - 133.96: 140 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: 222 2.45 - 3.06: 14863 3.06 - 3.67: 28560 3.67 - 4.29: 41763 4.29 - 4.90: 59929 Nonbonded interactions: 145337 Sorted by model distance: nonbonded pdb=" OH TYR B 571 " pdb=" O VAL F 567 " model vdw 1.833 2.440 nonbonded pdb=" NE2 GLN F 341 " pdb=" O MET G 110 " model vdw 1.905 2.520 nonbonded pdb=" OG SER A 179 " pdb=" F1 GB9 A1001 " model vdw 1.973 2.390 nonbonded pdb=" OG SER B 179 " pdb=" F1 GB9 B1001 " model vdw 1.973 2.390 nonbonded pdb=" OG SER F 179 " pdb=" F1 GB9 F1001 " model vdw 1.973 2.390 ... (remaining 145332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.580 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: 3.800 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 46.520 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.340 ------------------------------------------------------------------------------- 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= 0.506 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 : 1.948 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: 0.2967 time to fit residues: 166.3241 Evaluate side-chains 286 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN H 42 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 328 HIS ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN B 591 GLN C 42 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 324 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16324 Z= 0.340 Angle : 0.708 12.063 22012 Z= 0.381 Chirality : 0.042 0.199 2404 Planarity : 0.005 0.049 2780 Dihedral : 4.794 21.763 2180 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 34.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.29 % Allowed : 14.88 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 1936 helix: -0.39 (0.12), residues: 1524 sheet: None (None), residues: 0 loop : -1.56 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 344 HIS 0.007 0.001 HIS B 324 PHE 0.018 0.002 PHE B 297 TYR 0.022 0.002 TYR B 571 ARG 0.009 0.001 ARG F 581 *********************** 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 417 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 345 time to evaluate : 1.904 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 83 ASN cc_start: 0.9565 (t0) cc_final: 0.9173 (p0) REVERT: A 130 GLU cc_start: 0.9233 (tt0) cc_final: 0.8669 (tp30) REVERT: A 172 ASP cc_start: 0.8841 (t70) cc_final: 0.8545 (t0) REVERT: A 273 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9146 (tp) REVERT: A 341 GLN cc_start: 0.8700 (mt0) cc_final: 0.8274 (mt0) REVERT: B 83 ASN cc_start: 0.9553 (t0) cc_final: 0.9199 (p0) REVERT: B 174 MET cc_start: 0.8621 (ttt) cc_final: 0.8411 (tmm) REVERT: B 293 LEU cc_start: 0.9478 (pp) cc_final: 0.9177 (pp) REVERT: D 83 ASN cc_start: 0.9530 (t0) cc_final: 0.9147 (p0) REVERT: D 172 ASP cc_start: 0.8929 (t70) cc_final: 0.8435 (t0) REVERT: D 319 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8860 (tmtt) REVERT: E 72 MET cc_start: 0.5626 (ptt) cc_final: 0.5395 (ptt) REVERT: F 83 ASN cc_start: 0.9560 (t0) cc_final: 0.9211 (p0) REVERT: F 174 MET cc_start: 0.8641 (ttt) cc_final: 0.8387 (tmm) REVERT: F 293 LEU cc_start: 0.9508 (pp) cc_final: 0.9224 (pp) REVERT: F 319 LYS cc_start: 0.9057 (tttt) cc_final: 0.8722 (tmtt) REVERT: F 570 GLN cc_start: 0.8260 (tt0) cc_final: 0.8006 (tt0) outliers start: 72 outliers final: 47 residues processed: 378 average time/residue: 0.2700 time to fit residues: 149.8594 Evaluate side-chains 347 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 299 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER 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 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 GLU 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 C residue 132 ASP 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 241 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 266 ASP 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 233 VAL Chi-restraints excluded: chain F residue 241 LEU 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 292 LEU 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 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: 20.0000 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 48 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 overall best weight: 4.3586 ------------------------------------------------------------------------------- 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16324 Z= 0.277 Angle : 0.641 12.111 22012 Z= 0.344 Chirality : 0.039 0.189 2404 Planarity : 0.004 0.039 2780 Dihedral : 4.618 22.192 2180 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.24 % Allowed : 17.74 % Favored : 77.02 % 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 (0.18), residues: 1936 helix: 0.24 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : -1.36 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 344 HIS 0.006 0.001 HIS B 328 PHE 0.015 0.002 PHE D 297 TYR 0.021 0.002 TYR B 571 ARG 0.004 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 430 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 342 time to evaluate : 2.149 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: A 172 ASP cc_start: 0.8858 (t70) cc_final: 0.8619 (t0) REVERT: A 273 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9108 (tp) REVERT: A 293 LEU cc_start: 0.9352 (pp) cc_final: 0.9132 (pp) REVERT: A 570 GLN cc_start: 0.8208 (tt0) cc_final: 0.7860 (tt0) REVERT: H 101 ILE cc_start: 0.4586 (OUTLIER) cc_final: 0.3936 (mm) REVERT: B 81 LEU cc_start: 0.9339 (mm) cc_final: 0.9119 (pp) REVERT: B 174 MET cc_start: 0.8639 (ttt) cc_final: 0.8314 (tmm) REVERT: B 293 LEU cc_start: 0.9402 (pp) cc_final: 0.9096 (pp) REVERT: C 38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8272 (mmt-90) REVERT: C 52 MET cc_start: 0.0664 (tpp) cc_final: 0.0297 (mmt) REVERT: D 172 ASP cc_start: 0.8872 (t70) cc_final: 0.8491 (t0) REVERT: D 174 MET cc_start: 0.8612 (ttt) cc_final: 0.8369 (tmm) REVERT: D 319 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8739 (tmtt) REVERT: D 341 GLN cc_start: 0.8817 (mt0) cc_final: 0.8489 (mt0) REVERT: E 73 MET cc_start: 0.1644 (tpt) cc_final: 0.1132 (ptt) REVERT: F 81 LEU cc_start: 0.9353 (mm) cc_final: 0.9106 (pp) REVERT: F 174 MET cc_start: 0.8663 (ttt) cc_final: 0.8344 (tmm) REVERT: F 273 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9139 (tp) REVERT: F 293 LEU cc_start: 0.9430 (pp) cc_final: 0.9137 (pp) REVERT: F 319 LYS cc_start: 0.9041 (tttt) cc_final: 0.8693 (tmtt) REVERT: F 570 GLN cc_start: 0.8259 (tt0) cc_final: 0.7881 (tt0) REVERT: G 46 GLU cc_start: 0.8134 (pp20) cc_final: 0.7852 (tp30) REVERT: G 52 MET cc_start: 0.0074 (mmt) cc_final: -0.0246 (mmt) outliers start: 88 outliers final: 59 residues processed: 386 average time/residue: 0.2616 time to fit residues: 151.0806 Evaluate side-chains 368 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 305 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 106 CYS 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 240 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 273 ILE 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 A residue 575 HIS 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 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 322 GLU 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 38 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 147 THR 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 263 THR Chi-restraints excluded: chain D residue 266 ASP 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 D residue 586 GLN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain F residue 105 SER 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 266 ASP 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 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 108 HIS Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 50.0000 chunk 131 optimal weight: 50.0000 chunk 90 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 185 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN B 204 GLN B 321 GLN B 591 GLN C 61 ASN C 112 ASN D 204 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 HIS E 61 ASN E 112 ASN F 204 GLN F 321 GLN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN G 61 ASN G 112 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16324 Z= 0.184 Angle : 0.620 12.013 22012 Z= 0.321 Chirality : 0.038 0.211 2404 Planarity : 0.003 0.037 2780 Dihedral : 4.279 21.699 2180 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.17 % Allowed : 18.75 % Favored : 77.08 % 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: 0.64 (0.19), residues: 1936 helix: 0.92 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 288 HIS 0.003 0.000 HIS B 575 PHE 0.017 0.001 PHE A 548 TYR 0.022 0.002 TYR B 571 ARG 0.003 0.000 ARG B 325 *********************** 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 452 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 382 time to evaluate : 1.946 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 202 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: A 293 LEU cc_start: 0.9187 (pp) cc_final: 0.8974 (pp) REVERT: A 319 LYS cc_start: 0.8989 (tttt) cc_final: 0.8650 (tmtt) REVERT: B 293 LEU cc_start: 0.9203 (pp) cc_final: 0.8895 (pp) REVERT: B 319 LYS cc_start: 0.9025 (tttt) cc_final: 0.8748 (tmtt) REVERT: C 52 MET cc_start: 0.0425 (tpp) cc_final: 0.0130 (mmt) REVERT: C 93 PHE cc_start: 0.8284 (m-10) cc_final: 0.7913 (m-80) REVERT: D 172 ASP cc_start: 0.8824 (t70) cc_final: 0.8536 (t0) REVERT: D 174 MET cc_start: 0.8662 (ttt) cc_final: 0.8293 (tmm) REVERT: D 202 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: D 319 LYS cc_start: 0.9011 (tmtt) cc_final: 0.8751 (tmtt) REVERT: D 322 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: D 341 GLN cc_start: 0.8762 (mt0) cc_final: 0.8164 (tt0) REVERT: E 52 MET cc_start: 0.0587 (mmt) cc_final: 0.0253 (mmp) REVERT: E 73 MET cc_start: 0.1997 (tpt) cc_final: 0.1574 (ptt) REVERT: F 293 LEU cc_start: 0.9243 (pp) cc_final: 0.8948 (pp) REVERT: F 319 LYS cc_start: 0.9050 (tttt) cc_final: 0.8730 (tmtt) REVERT: F 322 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: F 323 GLN cc_start: 0.9004 (tp40) cc_final: 0.7990 (tp40) REVERT: F 570 GLN cc_start: 0.8054 (tt0) cc_final: 0.7806 (tt0) REVERT: G 46 GLU cc_start: 0.8211 (pp20) cc_final: 0.7794 (mm-30) REVERT: G 93 PHE cc_start: 0.8241 (m-10) cc_final: 0.7840 (m-80) outliers start: 70 outliers final: 44 residues processed: 414 average time/residue: 0.2785 time to fit residues: 173.6986 Evaluate side-chains 354 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 306 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 243 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 108 HIS Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 147 THR 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 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 108 HIS Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 151 CYS 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 322 GLU Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 112 ASN 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 322 GLU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS 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 112 ASN Chi-restraints excluded: chain G residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN B 575 HIS C 112 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 HIS E 42 GLN E 112 ASN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16324 Z= 0.254 Angle : 0.649 10.343 22012 Z= 0.345 Chirality : 0.039 0.185 2404 Planarity : 0.004 0.045 2780 Dihedral : 4.414 20.812 2180 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.24 % Allowed : 21.61 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1936 helix: 0.78 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.11 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 288 HIS 0.006 0.001 HIS D 575 PHE 0.034 0.002 PHE A 548 TYR 0.020 0.002 TYR B 571 ARG 0.004 0.000 ARG B 581 *********************** 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 413 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 325 time to evaluate : 1.906 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: A 202 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: A 570 GLN cc_start: 0.8245 (tt0) cc_final: 0.7922 (tt0) REVERT: H 52 MET cc_start: 0.0107 (mmt) cc_final: -0.0217 (mmt) REVERT: H 101 ILE cc_start: 0.3947 (OUTLIER) cc_final: 0.3062 (mm) REVERT: B 172 ASP cc_start: 0.8805 (t70) cc_final: 0.8474 (t0) REVERT: B 293 LEU cc_start: 0.9264 (pp) cc_final: 0.9019 (pp) REVERT: C 101 ILE cc_start: 0.4496 (OUTLIER) cc_final: 0.3871 (mm) REVERT: D 174 MET cc_start: 0.8676 (ttt) cc_final: 0.8328 (tmm) REVERT: D 319 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8699 (tmtt) REVERT: D 341 GLN cc_start: 0.8790 (mt0) cc_final: 0.8181 (tt0) REVERT: E 52 MET cc_start: 0.0675 (mmt) cc_final: 0.0201 (mmp) REVERT: E 101 ILE cc_start: 0.4240 (OUTLIER) cc_final: 0.3603 (mm) REVERT: F 293 LEU cc_start: 0.9304 (pp) cc_final: 0.9071 (pp) REVERT: F 319 LYS cc_start: 0.9024 (tttt) cc_final: 0.8625 (tmtt) REVERT: F 323 GLN cc_start: 0.8987 (tp40) cc_final: 0.8160 (tp40) REVERT: F 570 GLN cc_start: 0.8018 (tt0) cc_final: 0.7698 (tt0) REVERT: G 46 GLU cc_start: 0.8186 (pp20) cc_final: 0.7794 (mm-30) outliers start: 88 outliers final: 58 residues processed: 372 average time/residue: 0.2532 time to fit residues: 140.6263 Evaluate side-chains 355 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 293 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 219 LYS Chi-restraints excluded: chain A residue 240 PHE 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 299 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 550 VAL 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 112 ASN 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 151 CYS 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 299 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 MET 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 112 ASN Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 151 CYS 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 299 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 328 HIS 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 F residue 106 CYS Chi-restraints excluded: chain F residue 142 PHE Chi-restraints excluded: chain F residue 151 CYS Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 299 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 Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 108 HIS Chi-restraints excluded: chain G residue 112 ASN 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: 5.9990 chunk 167 optimal weight: 0.9990 chunk 36 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 185 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN C 112 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16324 Z= 0.217 Angle : 0.667 10.818 22012 Z= 0.347 Chirality : 0.041 0.185 2404 Planarity : 0.004 0.047 2780 Dihedral : 4.474 19.646 2180 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.42 % Allowed : 22.32 % Favored : 72.26 % 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: 0.65 (0.19), residues: 1936 helix: 0.87 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 344 HIS 0.005 0.001 HIS D 328 PHE 0.022 0.002 PHE C 69 TYR 0.019 0.002 TYR F 141 ARG 0.002 0.000 ARG D 581 *********************** 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: 91 poor density : 327 time to evaluate : 1.826 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: A 127 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7771 (t80) REVERT: A 174 MET cc_start: 0.8654 (ttt) cc_final: 0.8354 (tmm) REVERT: A 202 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8771 (m-80) REVERT: A 570 GLN cc_start: 0.8208 (tt0) cc_final: 0.7854 (tt0) REVERT: A 583 LYS cc_start: 0.9622 (mmtt) cc_final: 0.9325 (tptt) REVERT: H 52 MET cc_start: 0.0124 (mmt) cc_final: -0.0098 (mmt) REVERT: H 101 ILE cc_start: 0.3788 (OUTLIER) cc_final: 0.2613 (mm) REVERT: B 81 LEU cc_start: 0.9353 (mt) cc_final: 0.8965 (pp) REVERT: B 172 ASP cc_start: 0.8839 (t70) cc_final: 0.8482 (t0) REVERT: B 231 GLU cc_start: 0.8428 (pm20) cc_final: 0.8140 (pm20) REVERT: B 293 LEU cc_start: 0.9227 (pp) cc_final: 0.8996 (pp) REVERT: C 101 ILE cc_start: 0.4462 (OUTLIER) cc_final: 0.3935 (mm) REVERT: D 319 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8698 (tmtt) REVERT: D 322 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: D 341 GLN cc_start: 0.8736 (mt0) cc_final: 0.8235 (tt0) REVERT: E 52 MET cc_start: 0.0648 (mmt) cc_final: 0.0174 (mmp) REVERT: E 101 ILE cc_start: 0.4276 (OUTLIER) cc_final: 0.3455 (mt) REVERT: E 125 MET cc_start: 0.7894 (mtt) cc_final: 0.7413 (tpp) REVERT: F 81 LEU cc_start: 0.9347 (mt) cc_final: 0.8911 (pp) REVERT: F 293 LEU cc_start: 0.9264 (pp) cc_final: 0.9058 (pp) REVERT: F 319 LYS cc_start: 0.9018 (tttt) cc_final: 0.8619 (tmtt) REVERT: F 322 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: F 323 GLN cc_start: 0.8992 (tp40) cc_final: 0.8027 (tp40) REVERT: G 12 GLU cc_start: 0.0908 (OUTLIER) cc_final: 0.0605 (tm-30) REVERT: G 101 ILE cc_start: 0.4230 (OUTLIER) cc_final: 0.3602 (mt) outliers start: 91 outliers final: 67 residues processed: 378 average time/residue: 0.2583 time to fit residues: 146.2924 Evaluate side-chains 389 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 219 LYS 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 296 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 334 ASN 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 112 ASN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 151 CYS 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 299 LEU Chi-restraints excluded: chain B residue 322 GLU 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 112 ASN Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 151 CYS 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 299 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 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 151 CYS 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 292 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 299 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 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 112 ASN 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: 1.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN C 112 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16324 Z= 0.211 Angle : 0.692 11.928 22012 Z= 0.356 Chirality : 0.041 0.177 2404 Planarity : 0.004 0.040 2780 Dihedral : 4.485 26.400 2180 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.88 % Allowed : 23.33 % Favored : 71.79 % 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: 0.68 (0.19), residues: 1936 helix: 0.90 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.08 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 344 HIS 0.006 0.001 HIS D 328 PHE 0.021 0.002 PHE F 555 TYR 0.025 0.002 TYR D 141 ARG 0.007 0.000 ARG C 91 *********************** 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 414 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 332 time to evaluate : 1.909 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 127 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7772 (t80) REVERT: A 174 MET cc_start: 0.8624 (ttt) cc_final: 0.8346 (tmm) REVERT: A 202 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: A 570 GLN cc_start: 0.8233 (tt0) cc_final: 0.7846 (tt0) REVERT: H 52 MET cc_start: -0.0001 (mmt) cc_final: -0.0248 (mmt) REVERT: H 101 ILE cc_start: 0.4020 (OUTLIER) cc_final: 0.3432 (mp) REVERT: B 81 LEU cc_start: 0.9398 (mt) cc_final: 0.9045 (pp) REVERT: B 172 ASP cc_start: 0.8818 (t70) cc_final: 0.8429 (t0) REVERT: B 293 LEU cc_start: 0.9211 (pp) cc_final: 0.8992 (pp) REVERT: B 570 GLN cc_start: 0.8204 (tt0) cc_final: 0.7879 (tt0) REVERT: C 101 ILE cc_start: 0.4497 (OUTLIER) cc_final: 0.3884 (mm) REVERT: D 248 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.6698 (t80) REVERT: D 319 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8662 (tmtt) REVERT: D 322 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: D 546 MET cc_start: 0.9356 (ptp) cc_final: 0.9012 (ptp) REVERT: E 55 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5829 (pt0) REVERT: E 101 ILE cc_start: 0.4177 (OUTLIER) cc_final: 0.3141 (mt) REVERT: E 125 MET cc_start: 0.7879 (mtt) cc_final: 0.7394 (tpp) REVERT: F 81 LEU cc_start: 0.9379 (mt) cc_final: 0.9067 (pp) REVERT: F 231 GLU cc_start: 0.8408 (pm20) cc_final: 0.8115 (pm20) REVERT: F 293 LEU cc_start: 0.9271 (pp) cc_final: 0.9064 (pp) REVERT: F 319 LYS cc_start: 0.9011 (tttt) cc_final: 0.8626 (tmtt) REVERT: F 323 GLN cc_start: 0.9002 (tp40) cc_final: 0.7969 (tp40) REVERT: G 12 GLU cc_start: 0.0978 (OUTLIER) cc_final: 0.0620 (tm-30) REVERT: G 101 ILE cc_start: 0.4111 (OUTLIER) cc_final: 0.3327 (mt) outliers start: 82 outliers final: 60 residues processed: 377 average time/residue: 0.2652 time to fit residues: 148.2488 Evaluate side-chains 377 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 308 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 219 LYS 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 299 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 334 ASN 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 109 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 575 HIS 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 151 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 266 ASP 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 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 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 151 CYS Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 567 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 0.0170 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- 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 61 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16324 Z= 0.257 Angle : 0.741 13.492 22012 Z= 0.382 Chirality : 0.041 0.237 2404 Planarity : 0.004 0.037 2780 Dihedral : 4.599 38.731 2180 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.88 % Allowed : 24.17 % Favored : 70.95 % 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: 0.62 (0.19), residues: 1936 helix: 0.83 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.94 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 344 HIS 0.003 0.001 HIS F 228 PHE 0.043 0.002 PHE B 548 TYR 0.024 0.002 TYR D 141 ARG 0.006 0.000 ARG C 91 *********************** 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 409 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 327 time to evaluate : 1.952 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: 0.9380 (mt) cc_final: 0.9007 (pp) REVERT: A 127 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 174 MET cc_start: 0.8636 (ttt) cc_final: 0.8331 (tmm) REVERT: A 202 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8747 (m-80) REVERT: A 237 TYR cc_start: 0.8282 (t80) cc_final: 0.8073 (t80) REVERT: A 570 GLN cc_start: 0.8324 (tt0) cc_final: 0.7921 (tt0) REVERT: H 52 MET cc_start: 0.0329 (mmt) cc_final: 0.0042 (mmt) REVERT: H 73 MET cc_start: 0.1779 (tpt) cc_final: 0.1477 (ptt) REVERT: H 91 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8683 (mmt-90) REVERT: H 101 ILE cc_start: 0.4257 (OUTLIER) cc_final: 0.3614 (mp) REVERT: B 81 LEU cc_start: 0.9418 (mt) cc_final: 0.9103 (pp) REVERT: B 172 ASP cc_start: 0.8825 (t70) cc_final: 0.8445 (t0) REVERT: B 231 GLU cc_start: 0.8473 (pm20) cc_final: 0.8211 (pm20) REVERT: B 293 LEU cc_start: 0.9243 (pp) cc_final: 0.9000 (pp) REVERT: B 570 GLN cc_start: 0.8223 (tt0) cc_final: 0.7866 (tt0) REVERT: C 101 ILE cc_start: 0.5094 (OUTLIER) cc_final: 0.4653 (mm) REVERT: D 248 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.6817 (t80) REVERT: D 319 LYS cc_start: 0.8992 (tmtt) cc_final: 0.8638 (tmtt) REVERT: D 570 GLN cc_start: 0.8371 (tt0) cc_final: 0.8014 (tt0) REVERT: D 585 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7827 (mt) REVERT: E 101 ILE cc_start: 0.3938 (OUTLIER) cc_final: 0.2920 (mt) REVERT: E 125 MET cc_start: 0.7837 (mtt) cc_final: 0.7449 (tpp) REVERT: F 81 LEU cc_start: 0.9430 (mt) cc_final: 0.9086 (pp) REVERT: F 172 ASP cc_start: 0.8868 (t70) cc_final: 0.8508 (t70) REVERT: F 293 LEU cc_start: 0.9284 (pp) cc_final: 0.9062 (pp) REVERT: G 12 GLU cc_start: 0.0880 (OUTLIER) cc_final: 0.0541 (tm-30) REVERT: G 101 ILE cc_start: 0.4192 (OUTLIER) cc_final: 0.3219 (mt) REVERT: G 110 MET cc_start: 0.7917 (mmm) cc_final: 0.7625 (mmm) REVERT: G 125 MET cc_start: 0.7721 (mtt) cc_final: 0.7073 (tpp) outliers start: 82 outliers final: 66 residues processed: 378 average time/residue: 0.2744 time to fit residues: 155.4032 Evaluate side-chains 385 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 310 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 334 ASN 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 105 SER 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 151 CYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 266 ASP 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 299 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 575 HIS 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 151 CYS Chi-restraints excluded: chain D residue 202 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 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 299 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 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 151 CYS Chi-restraints excluded: chain F residue 243 LEU 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 322 GLU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 567 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 50.0000 chunk 135 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 ASN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** 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: 0.7736 moved from start: 0.6037 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= 0.243 Angle : 0.753 13.964 22012 Z= 0.383 Chirality : 0.041 0.223 2404 Planarity : 0.003 0.055 2780 Dihedral : 4.655 42.269 2180 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.52 % Allowed : 25.24 % Favored : 70.24 % 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: 0.65 (0.19), residues: 1936 helix: 0.87 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.03 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 344 HIS 0.002 0.001 HIS F 228 PHE 0.039 0.002 PHE D 555 TYR 0.024 0.002 TYR A 141 ARG 0.004 0.000 ARG C 91 *********************** 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 401 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 325 time to evaluate : 2.075 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 81 LEU cc_start: 0.9351 (mt) cc_final: 0.9007 (pp) REVERT: A 127 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 174 MET cc_start: 0.8654 (ttt) cc_final: 0.8295 (tmm) REVERT: A 202 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: A 237 TYR cc_start: 0.8261 (t80) cc_final: 0.7979 (t80) REVERT: A 570 GLN cc_start: 0.8292 (tt0) cc_final: 0.7848 (tt0) REVERT: H 52 MET cc_start: 0.0260 (mmt) cc_final: 0.0027 (mmt) REVERT: H 73 MET cc_start: 0.1839 (tpt) cc_final: 0.1554 (ptt) REVERT: H 101 ILE cc_start: 0.4315 (OUTLIER) cc_final: 0.3634 (mp) REVERT: B 81 LEU cc_start: 0.9416 (mt) cc_final: 0.9122 (pp) REVERT: B 172 ASP cc_start: 0.8801 (t70) cc_final: 0.8506 (t0) REVERT: B 231 GLU cc_start: 0.8438 (pm20) cc_final: 0.8145 (pm20) REVERT: B 248 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7120 (t80) REVERT: B 293 LEU cc_start: 0.9202 (pp) cc_final: 0.8964 (pp) REVERT: B 570 GLN cc_start: 0.8294 (tt0) cc_final: 0.7885 (tt0) REVERT: C 101 ILE cc_start: 0.4938 (OUTLIER) cc_final: 0.4605 (mm) REVERT: D 248 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6759 (t80) REVERT: D 319 LYS cc_start: 0.8996 (tmtt) cc_final: 0.8636 (tmtt) REVERT: D 322 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: D 341 GLN cc_start: 0.9114 (mt0) cc_final: 0.7736 (tt0) REVERT: D 570 GLN cc_start: 0.8340 (tt0) cc_final: 0.8026 (tt0) REVERT: D 585 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7869 (mt) REVERT: E 55 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5956 (pt0) REVERT: E 101 ILE cc_start: 0.3916 (OUTLIER) cc_final: 0.3454 (mp) REVERT: F 172 ASP cc_start: 0.8839 (t70) cc_final: 0.8467 (t70) REVERT: F 293 LEU cc_start: 0.9256 (pp) cc_final: 0.9032 (pp) REVERT: F 548 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6656 (t80) REVERT: G 12 GLU cc_start: 0.0879 (OUTLIER) cc_final: 0.0562 (tm-30) REVERT: G 73 MET cc_start: 0.1988 (tpt) cc_final: 0.1592 (ptt) REVERT: G 101 ILE cc_start: 0.4093 (OUTLIER) cc_final: 0.3197 (mt) REVERT: G 125 MET cc_start: 0.7694 (mtt) cc_final: 0.6845 (tpt) outliers start: 76 outliers final: 59 residues processed: 370 average time/residue: 0.2697 time to fit residues: 149.2494 Evaluate side-chains 382 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 311 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 334 ASN 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 105 SER 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 151 CYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 266 ASP 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 322 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 575 HIS 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 151 CYS 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 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 THR 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 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 151 CYS Chi-restraints excluded: chain F residue 243 LEU 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 322 GLU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 548 PHE Chi-restraints excluded: chain F residue 567 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: 8.9990 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 126 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 ASN ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16324 Z= 0.204 Angle : 0.785 15.325 22012 Z= 0.391 Chirality : 0.042 0.255 2404 Planarity : 0.003 0.054 2780 Dihedral : 4.523 40.784 2180 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.86 % Allowed : 27.50 % Favored : 69.64 % 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: 0.97 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 344 HIS 0.005 0.001 HIS A 328 PHE 0.047 0.002 PHE B 555 TYR 0.020 0.001 TYR B 571 ARG 0.007 0.000 ARG H 87 ********************** 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 389 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 341 time to evaluate : 1.821 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 127 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7720 (t80) REVERT: A 174 MET cc_start: 0.8673 (ttt) cc_final: 0.8277 (tmm) REVERT: A 319 LYS cc_start: 0.8936 (tttt) cc_final: 0.8621 (tmtt) REVERT: A 553 ARG cc_start: 0.9246 (mmp-170) cc_final: 0.8870 (mmp80) REVERT: A 570 GLN cc_start: 0.8387 (tt0) cc_final: 0.7535 (tt0) REVERT: A 583 LYS cc_start: 0.9433 (pptt) cc_final: 0.9153 (tptt) REVERT: H 52 MET cc_start: 0.0186 (mmt) cc_final: -0.0042 (mmt) REVERT: H 101 ILE cc_start: 0.4114 (OUTLIER) cc_final: 0.3452 (mp) REVERT: B 248 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 293 LEU cc_start: 0.9044 (pp) cc_final: 0.8828 (pp) REVERT: B 319 LYS cc_start: 0.8971 (tttt) cc_final: 0.8740 (tmtt) REVERT: B 569 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9044 (mp0) REVERT: B 570 GLN cc_start: 0.8266 (tt0) cc_final: 0.8055 (tt0) REVERT: C 101 ILE cc_start: 0.4823 (OUTLIER) cc_final: 0.4471 (mm) REVERT: D 248 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6525 (t80) REVERT: D 319 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8620 (tmtt) REVERT: D 322 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: D 553 ARG cc_start: 0.9403 (mmp-170) cc_final: 0.9143 (mmp80) REVERT: D 570 GLN cc_start: 0.8321 (tt0) cc_final: 0.8101 (tt0) REVERT: D 585 LEU cc_start: 0.8285 (tt) cc_final: 0.7999 (mt) REVERT: E 73 MET cc_start: 0.2628 (tpt) cc_final: 0.2278 (mmt) REVERT: E 101 ILE cc_start: 0.3812 (OUTLIER) cc_final: 0.3155 (mp) REVERT: F 172 ASP cc_start: 0.8772 (t70) cc_final: 0.8468 (t0) REVERT: F 248 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6924 (t80) REVERT: F 548 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6701 (t80) REVERT: G 12 GLU cc_start: 0.0614 (OUTLIER) cc_final: 0.0278 (tm-30) REVERT: G 72 MET cc_start: 0.5096 (ptm) cc_final: 0.4647 (ptm) REVERT: G 101 ILE cc_start: 0.4096 (OUTLIER) cc_final: 0.3304 (mt) REVERT: G 125 MET cc_start: 0.7593 (mtt) cc_final: 0.6866 (tpt) outliers start: 48 outliers final: 33 residues processed: 371 average time/residue: 0.2765 time to fit residues: 150.0508 Evaluate side-chains 358 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 314 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 334 ASN 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 109 LEU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 322 GLU 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 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 151 CYS Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 151 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 327 LYS Chi-restraints excluded: chain F residue 548 PHE Chi-restraints excluded: chain F residue 567 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 162 optimal weight: 5.9990 chunk 46 optimal weight: 0.0470 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 50.0000 chunk 133 optimal weight: 9.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.157440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.139403 restraints weight = 82585.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.138489 restraints weight = 51716.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.139022 restraints weight = 52217.467| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16324 Z= 0.236 Angle : 0.819 19.493 22012 Z= 0.410 Chirality : 0.043 0.234 2404 Planarity : 0.003 0.044 2780 Dihedral : 4.648 43.865 2180 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.92 % Allowed : 28.10 % Favored : 68.99 % 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: 0.74 (0.19), residues: 1936 helix: 0.88 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 344 HIS 0.009 0.001 HIS A 328 PHE 0.035 0.002 PHE B 555 TYR 0.025 0.001 TYR A 141 ARG 0.010 0.000 ARG D 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.44 seconds wall clock time: 62 minutes 36.09 seconds (3756.09 seconds total)