Starting phenix.real_space_refine on Fri Mar 15 19:20:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d67_27219/03_2024/8d67_27219_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d67_27219/03_2024/8d67_27219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d67_27219/03_2024/8d67_27219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d67_27219/03_2024/8d67_27219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d67_27219/03_2024/8d67_27219_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d67_27219/03_2024/8d67_27219_neut_updated.pdb" } resolution = 3.3 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 8195 2.51 5 N 2085 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 13": "OD1" <-> "OD2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2510 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2510 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2510 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2510 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2510 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.81, per 1000 atoms: 0.54 Number of scatterers: 12570 At special positions: 0 Unit cell: (89.1, 89.1, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2255 8.00 N 2085 7.00 C 8195 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=0, symmetry=0 Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.5 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 20 sheets defined 28.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.82 Creating SS restraints... Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.623A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 249 removed outlier: 3.626A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.624A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 249 removed outlier: 3.626A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 210 through 224 removed outlier: 3.622A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 249 removed outlier: 3.626A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 284 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 210 through 224 removed outlier: 3.624A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 249 removed outlier: 3.625A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 284 Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'E' and resid 64 through 67 No H-bonds generated for 'chain 'E' and resid 64 through 67' Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 210 through 224 removed outlier: 3.623A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.626A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 284 Processing helix chain 'E' and resid 303 through 316 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.682A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'A' and resid 166 through 174 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.682A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'B' and resid 166 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.682A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' and resid 166 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.683A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'D' and resid 166 through 174 Processing sheet with id= Q, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.682A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'E' and resid 166 through 174 505 hydrogen bonds defined for protein. 1500 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: 3.47 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2765 1.33 - 1.45: 3066 1.45 - 1.57: 7024 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 12910 Sorted by residual: bond pdb=" C GLU C 59 " pdb=" O GLU C 59 " ideal model delta sigma weight residual 1.234 1.205 0.029 1.07e-02 8.73e+03 7.30e+00 bond pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.31e-02 5.83e+03 7.25e+00 bond pdb=" CA GLN E 62 " pdb=" C GLN E 62 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.31e-02 5.83e+03 7.23e+00 bond pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.31e-02 5.83e+03 7.18e+00 bond pdb=" C GLU E 59 " pdb=" O GLU E 59 " ideal model delta sigma weight residual 1.234 1.206 0.029 1.07e-02 8.73e+03 7.13e+00 ... (remaining 12905 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.61: 220 104.61 - 112.13: 6105 112.13 - 119.66: 4604 119.66 - 127.18: 6482 127.18 - 134.70: 174 Bond angle restraints: 17585 Sorted by residual: angle pdb=" N GLN B 62 " pdb=" CA GLN B 62 " pdb=" C GLN B 62 " ideal model delta sigma weight residual 113.61 101.36 12.25 1.50e+00 4.44e-01 6.67e+01 angle pdb=" N GLN D 62 " pdb=" CA GLN D 62 " pdb=" C GLN D 62 " ideal model delta sigma weight residual 113.61 101.36 12.25 1.50e+00 4.44e-01 6.67e+01 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 113.61 101.40 12.21 1.50e+00 4.44e-01 6.63e+01 angle pdb=" N GLN C 62 " pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 113.61 101.40 12.21 1.50e+00 4.44e-01 6.63e+01 angle pdb=" N GLN E 62 " pdb=" CA GLN E 62 " pdb=" C GLN E 62 " ideal model delta sigma weight residual 113.61 101.40 12.21 1.50e+00 4.44e-01 6.62e+01 ... (remaining 17580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6784 17.66 - 35.33: 631 35.33 - 52.99: 105 52.99 - 70.66: 10 70.66 - 88.32: 10 Dihedral angle restraints: 7540 sinusoidal: 3030 harmonic: 4510 Sorted by residual: dihedral pdb=" CA SER A 250 " pdb=" C SER A 250 " pdb=" N ASN A 251 " pdb=" CA ASN A 251 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER C 250 " pdb=" C SER C 250 " pdb=" N ASN C 251 " pdb=" CA ASN C 251 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER E 250 " pdb=" C SER E 250 " pdb=" N ASN E 251 " pdb=" CA ASN E 251 " ideal model delta harmonic sigma weight residual 180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1654 0.087 - 0.175: 251 0.175 - 0.262: 20 0.262 - 0.350: 15 0.350 - 0.437: 5 Chirality restraints: 1945 Sorted by residual: chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA PHE D 119 " pdb=" N PHE D 119 " pdb=" C PHE D 119 " pdb=" CB PHE D 119 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 1942 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " 0.014 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP A 206 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 206 " -0.014 2.00e-02 2.50e+03 1.49e-02 5.58e+00 pdb=" CG TRP D 206 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 206 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 206 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 206 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 206 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP D 206 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 206 " -0.013 2.00e-02 2.50e+03 1.49e-02 5.57e+00 pdb=" CG TRP C 206 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 206 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 206 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 206 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 206 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 206 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP C 206 " 0.003 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2999 2.79 - 3.32: 10679 3.32 - 3.84: 19885 3.84 - 4.37: 23676 4.37 - 4.90: 41997 Nonbonded interactions: 99236 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" OD2 ASP B 86 " model vdw 2.261 2.440 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.290 2.440 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.290 2.440 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.290 2.440 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.290 2.440 ... (remaining 99231 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 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.310 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 36.110 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.009 0.063 12910 Z= 0.601 Angle : 0.968 12.253 17585 Z= 0.560 Chirality : 0.070 0.437 1945 Planarity : 0.006 0.057 2240 Dihedral : 13.901 88.320 4630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.36 % Allowed : 0.73 % Favored : 98.91 % 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: -1.52 (0.21), residues: 1525 helix: -0.17 (0.24), residues: 460 sheet: -0.05 (0.25), residues: 480 loop : -2.52 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 206 HIS 0.005 0.001 HIS D 177 PHE 0.021 0.003 PHE A 208 TYR 0.022 0.003 TYR C 248 ARG 0.004 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.031 Fit side-chains REVERT: A 90 LYS cc_start: 0.8876 (pttm) cc_final: 0.8515 (pttm) REVERT: A 123 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7360 (ttm-80) REVERT: A 176 ASP cc_start: 0.7592 (m-30) cc_final: 0.7245 (m-30) REVERT: B 86 ASP cc_start: 0.8073 (t70) cc_final: 0.7643 (t70) REVERT: B 90 LYS cc_start: 0.8862 (pttm) cc_final: 0.8647 (pttm) REVERT: C 124 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7748 (mm110) REVERT: D 86 ASP cc_start: 0.8197 (t70) cc_final: 0.7983 (t70) REVERT: D 124 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7495 (mm-40) REVERT: E 86 ASP cc_start: 0.8117 (t70) cc_final: 0.7556 (t70) REVERT: E 90 LYS cc_start: 0.8788 (pttm) cc_final: 0.8533 (pttm) REVERT: E 123 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7369 (ttm-80) REVERT: E 208 PHE cc_start: 0.8357 (m-10) cc_final: 0.8097 (m-80) outliers start: 5 outliers final: 5 residues processed: 155 average time/residue: 0.3027 time to fit residues: 62.1375 Evaluate side-chains 117 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12910 Z= 0.225 Angle : 0.535 6.287 17585 Z= 0.272 Chirality : 0.047 0.148 1945 Planarity : 0.004 0.039 2240 Dihedral : 4.759 17.381 1705 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.65 % Allowed : 6.55 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1525 helix: 0.75 (0.25), residues: 460 sheet: 0.10 (0.25), residues: 480 loop : -2.41 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 206 HIS 0.003 0.001 HIS B 177 PHE 0.013 0.001 PHE E 121 TYR 0.011 0.001 TYR A 248 ARG 0.002 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.348 Fit side-chains REVERT: A 206 TRP cc_start: 0.7873 (p-90) cc_final: 0.5541 (m100) REVERT: A 252 ILE cc_start: 0.8086 (mt) cc_final: 0.7708 (pt) REVERT: B 86 ASP cc_start: 0.8090 (t70) cc_final: 0.7657 (t70) REVERT: B 90 LYS cc_start: 0.8729 (pttm) cc_final: 0.8511 (pttm) REVERT: B 114 MET cc_start: 0.7667 (mtt) cc_final: 0.7365 (mtt) REVERT: C 90 LYS cc_start: 0.8773 (pttm) cc_final: 0.8548 (pttm) REVERT: D 115 ASP cc_start: 0.8260 (t70) cc_final: 0.8027 (t70) REVERT: D 124 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7890 (mm-40) REVERT: E 86 ASP cc_start: 0.8033 (t70) cc_final: 0.7446 (t70) REVERT: E 208 PHE cc_start: 0.8408 (m-10) cc_final: 0.8136 (m-10) outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 0.3614 time to fit residues: 57.3764 Evaluate side-chains 115 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain E residue 252 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 121 optimal weight: 0.0170 chunk 135 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12910 Z= 0.242 Angle : 0.527 5.552 17585 Z= 0.268 Chirality : 0.047 0.148 1945 Planarity : 0.003 0.033 2240 Dihedral : 4.594 18.169 1695 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.82 % Allowed : 9.09 % Favored : 89.09 % 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: -0.66 (0.22), residues: 1525 helix: 1.17 (0.25), residues: 460 sheet: 0.31 (0.26), residues: 460 loop : -2.39 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 206 HIS 0.003 0.001 HIS A 177 PHE 0.012 0.001 PHE A 247 TYR 0.011 0.001 TYR B 245 ARG 0.002 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.197 Fit side-chains REVERT: A 59 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 239 MET cc_start: 0.5691 (ttm) cc_final: 0.5371 (ttm) REVERT: A 252 ILE cc_start: 0.8008 (mt) cc_final: 0.7620 (pt) REVERT: B 86 ASP cc_start: 0.8171 (t70) cc_final: 0.7724 (t70) REVERT: B 90 LYS cc_start: 0.8680 (pttm) cc_final: 0.8466 (pttm) REVERT: C 86 ASP cc_start: 0.7913 (t70) cc_final: 0.7638 (t70) REVERT: E 86 ASP cc_start: 0.8152 (t70) cc_final: 0.7582 (t70) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 0.3505 time to fit residues: 57.7653 Evaluate side-chains 123 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12910 Z= 0.265 Angle : 0.525 5.401 17585 Z= 0.268 Chirality : 0.047 0.148 1945 Planarity : 0.003 0.029 2240 Dihedral : 4.585 19.827 1695 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.38 % Allowed : 11.05 % Favored : 87.56 % 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: -0.50 (0.22), residues: 1525 helix: 1.39 (0.25), residues: 455 sheet: 0.35 (0.26), residues: 460 loop : -2.30 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 206 HIS 0.004 0.001 HIS C 177 PHE 0.012 0.001 PHE A 247 TYR 0.012 0.001 TYR C 261 ARG 0.002 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.372 Fit side-chains REVERT: A 59 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 86 ASP cc_start: 0.8144 (t70) cc_final: 0.7707 (t70) REVERT: B 90 LYS cc_start: 0.8694 (pttm) cc_final: 0.8479 (pttm) REVERT: C 114 MET cc_start: 0.8301 (mtt) cc_final: 0.7871 (mtt) REVERT: E 86 ASP cc_start: 0.8139 (t70) cc_final: 0.7561 (t70) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.3713 time to fit residues: 56.3669 Evaluate side-chains 111 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12910 Z= 0.242 Angle : 0.503 5.253 17585 Z= 0.257 Chirality : 0.046 0.147 1945 Planarity : 0.003 0.028 2240 Dihedral : 4.493 17.686 1695 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.69 % Allowed : 11.13 % Favored : 86.18 % 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: -0.52 (0.22), residues: 1525 helix: 1.10 (0.25), residues: 485 sheet: 0.67 (0.27), residues: 425 loop : -2.39 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.003 0.001 HIS A 177 PHE 0.011 0.001 PHE A 247 TYR 0.013 0.001 TYR E 245 ARG 0.002 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.350 Fit side-chains REVERT: A 59 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8345 (mm-30) REVERT: B 86 ASP cc_start: 0.8137 (t70) cc_final: 0.7701 (t70) REVERT: B 90 LYS cc_start: 0.8673 (pttm) cc_final: 0.8466 (pttm) REVERT: C 114 MET cc_start: 0.8284 (mtt) cc_final: 0.7849 (mtt) REVERT: E 86 ASP cc_start: 0.8143 (t70) cc_final: 0.7565 (t70) outliers start: 37 outliers final: 21 residues processed: 126 average time/residue: 0.3503 time to fit residues: 58.3237 Evaluate side-chains 130 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12910 Z= 0.200 Angle : 0.483 5.140 17585 Z= 0.246 Chirality : 0.046 0.150 1945 Planarity : 0.003 0.026 2240 Dihedral : 4.351 16.752 1695 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.96 % Allowed : 12.29 % Favored : 85.75 % 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: -0.39 (0.22), residues: 1525 helix: 1.24 (0.25), residues: 485 sheet: 0.79 (0.27), residues: 420 loop : -2.36 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.003 0.001 HIS C 177 PHE 0.010 0.001 PHE A 247 TYR 0.011 0.001 TYR E 245 ARG 0.002 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.429 Fit side-chains REVERT: A 59 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 86 ASP cc_start: 0.8140 (t70) cc_final: 0.7697 (t70) REVERT: C 114 MET cc_start: 0.8306 (mtt) cc_final: 0.7850 (mtt) REVERT: E 44 THR cc_start: 0.8746 (t) cc_final: 0.8527 (m) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.3533 time to fit residues: 62.0381 Evaluate side-chains 120 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 0.0070 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12910 Z= 0.329 Angle : 0.547 5.509 17585 Z= 0.280 Chirality : 0.048 0.149 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.652 19.656 1695 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.18 % Allowed : 12.95 % Favored : 84.87 % 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: -0.61 (0.22), residues: 1525 helix: 1.03 (0.24), residues: 515 sheet: 0.61 (0.27), residues: 425 loop : -2.61 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 206 HIS 0.004 0.001 HIS A 177 PHE 0.012 0.001 PHE A 19 TYR 0.011 0.002 TYR E 245 ARG 0.002 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.437 Fit side-chains REVERT: A 59 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8391 (mm-30) REVERT: B 86 ASP cc_start: 0.8071 (t70) cc_final: 0.7628 (t70) REVERT: C 114 MET cc_start: 0.8265 (mtt) cc_final: 0.7831 (mtt) outliers start: 30 outliers final: 24 residues processed: 122 average time/residue: 0.3542 time to fit residues: 57.4340 Evaluate side-chains 123 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 113 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12910 Z= 0.161 Angle : 0.472 5.105 17585 Z= 0.241 Chirality : 0.045 0.148 1945 Planarity : 0.003 0.024 2240 Dihedral : 4.288 15.849 1695 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.40 % Allowed : 12.73 % Favored : 84.87 % 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: -0.29 (0.22), residues: 1525 helix: 1.40 (0.25), residues: 475 sheet: 0.79 (0.27), residues: 420 loop : -2.26 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.003 0.001 HIS E 177 PHE 0.011 0.001 PHE B 208 TYR 0.012 0.001 TYR E 245 ARG 0.002 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.502 Fit side-chains REVERT: A 59 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 86 ASP cc_start: 0.8134 (t70) cc_final: 0.7683 (t70) REVERT: C 114 MET cc_start: 0.8233 (mtt) cc_final: 0.7797 (mtt) REVERT: E 44 THR cc_start: 0.8732 (t) cc_final: 0.8517 (m) outliers start: 33 outliers final: 24 residues processed: 128 average time/residue: 0.3653 time to fit residues: 62.0076 Evaluate side-chains 119 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12910 Z= 0.474 Angle : 0.617 6.907 17585 Z= 0.319 Chirality : 0.051 0.159 1945 Planarity : 0.004 0.025 2240 Dihedral : 4.991 23.743 1695 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.25 % Allowed : 13.24 % Favored : 84.51 % 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: -0.74 (0.22), residues: 1525 helix: 0.94 (0.24), residues: 515 sheet: 0.46 (0.27), residues: 425 loop : -2.63 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 206 HIS 0.005 0.001 HIS A 177 PHE 0.016 0.002 PHE A 19 TYR 0.016 0.002 TYR E 261 ARG 0.003 0.001 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.436 Fit side-chains REVERT: A 263 ASP cc_start: 0.7509 (t70) cc_final: 0.7207 (t0) REVERT: B 86 ASP cc_start: 0.7971 (t70) cc_final: 0.7557 (t70) REVERT: C 114 MET cc_start: 0.8298 (mtt) cc_final: 0.7879 (mtt) REVERT: C 144 ASP cc_start: 0.8412 (p0) cc_final: 0.8207 (p0) outliers start: 31 outliers final: 28 residues processed: 128 average time/residue: 0.3470 time to fit residues: 59.2770 Evaluate side-chains 132 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12910 Z= 0.158 Angle : 0.474 5.184 17585 Z= 0.243 Chirality : 0.046 0.155 1945 Planarity : 0.003 0.025 2240 Dihedral : 4.366 18.267 1695 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.53 % Allowed : 14.33 % Favored : 84.15 % 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: -0.43 (0.22), residues: 1525 helix: 1.18 (0.25), residues: 490 sheet: 0.74 (0.27), residues: 420 loop : -2.35 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.003 0.001 HIS E 177 PHE 0.012 0.001 PHE B 208 TYR 0.012 0.001 TYR E 245 ARG 0.001 0.000 ARG A 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.424 Fit side-chains REVERT: A 59 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 86 ASP cc_start: 0.8120 (t70) cc_final: 0.7676 (t70) REVERT: C 114 MET cc_start: 0.8245 (mtt) cc_final: 0.7810 (mtt) REVERT: C 206 TRP cc_start: 0.7847 (p-90) cc_final: 0.5199 (m100) REVERT: E 44 THR cc_start: 0.8742 (t) cc_final: 0.8523 (m) outliers start: 21 outliers final: 20 residues processed: 112 average time/residue: 0.3719 time to fit residues: 54.7613 Evaluate side-chains 117 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.173723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132357 restraints weight = 13008.802| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.60 r_work: 0.3250 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12910 Z= 0.180 Angle : 0.476 5.264 17585 Z= 0.244 Chirality : 0.046 0.152 1945 Planarity : 0.003 0.024 2240 Dihedral : 4.275 16.693 1695 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.75 % Allowed : 14.33 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1525 helix: 1.34 (0.26), residues: 480 sheet: 0.80 (0.27), residues: 420 loop : -2.29 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.003 0.001 HIS E 177 PHE 0.011 0.001 PHE B 208 TYR 0.010 0.001 TYR E 245 ARG 0.002 0.000 ARG B 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.20 seconds wall clock time: 42 minutes 49.10 seconds (2569.10 seconds total)