Starting phenix.real_space_refine on Thu Mar 21 15:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/03_2024/8x43_38041_neut_trim_updated.pdb" } resolution = 3.0 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= 0.003 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 C 9804 2.51 5 N 2572 2.21 5 O 2712 1.98 5 F 4 1.80 5 H 14984 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 566": "OD1" <-> "OD2" Residue "C ASP 577": "OD1" <-> "OD2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 566": "OD1" <-> "OD2" Residue "E ASP 577": "OD1" <-> "OD2" Residue "E ASP 590": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G ASP 566": "OD1" <-> "OD2" Residue "G ASP 577": "OD1" <-> "OD2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 140": "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: 30164 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.79, per 1000 atoms: 0.42 Number of scatterers: 30164 At special positions: 0 Unit cell: (125.55, 125.55, 120.9, 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) S 88 16.00 F 4 9.00 O 2712 8.00 N 2572 7.00 C 9804 6.00 H 14984 1.00 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: 26.62 Conformation dependent library (CDL) restraints added in 3.3 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 0 sheets defined 75.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 119 through 150 removed outlier: 4.016A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 167 through 181 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 326 removed outlier: 4.165A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 5.313A 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 539 through 560 Processing helix chain 'A' and resid 565 through 594 Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 92 through 114 Processing helix chain 'C' and resid 119 through 150 removed outlier: 4.015A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N CYS C 150 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 167 through 181 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 254 Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 288 through 326 removed outlier: 4.165A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'C' and resid 333 through 349 Processing helix chain 'C' and resid 539 through 561 Proline residue: C 561 - end of helix Processing helix chain 'C' and resid 564 through 594 Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'E' and resid 71 through 85 Processing helix chain 'E' and resid 92 through 114 Processing helix chain 'E' and resid 119 through 150 removed outlier: 4.018A pdb=" N ILE E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY E 149 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS E 150 " --> pdb=" O TRP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 165 Processing helix chain 'E' and resid 167 through 181 Processing helix chain 'E' and resid 196 through 211 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 254 Processing helix chain 'E' and resid 264 through 275 Processing helix chain 'E' and resid 288 through 326 removed outlier: 4.168A pdb=" N ILE E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) Proline residue: E 308 - end of helix Processing helix chain 'E' and resid 332 through 349 removed outlier: 3.736A pdb=" N ALA E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 560 Processing helix chain 'E' and resid 565 through 594 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 92 through 114 Processing helix chain 'G' and resid 119 through 150 removed outlier: 4.033A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N CYS G 150 " --> pdb=" O TRP G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 167 through 181 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 229 through 254 Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 326 removed outlier: 4.168A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 333 through 349 Processing helix chain 'G' and resid 539 through 560 Processing helix chain 'G' and resid 564 through 594 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 83 through 93 Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 140 through 147 1044 hydrogen bonds defined for protein. 3132 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: 11.36 Time building geometry restraints manager: 27.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14956 1.03 - 1.23: 39 1.23 - 1.42: 6685 1.42 - 1.62: 8660 1.62 - 1.81: 148 Bond restraints: 30488 Sorted by residual: bond pdb=" C10 7Q0 A 801 " pdb=" C4 7Q0 A 801 " ideal model delta sigma weight residual 1.468 1.382 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C10 7Q0 E 801 " pdb=" C4 7Q0 E 801 " ideal model delta sigma weight residual 1.468 1.383 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C10 7Q0 G 801 " pdb=" C4 7Q0 G 801 " ideal model delta sigma weight residual 1.468 1.383 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C10 7Q0 C 801 " pdb=" C4 7Q0 C 801 " ideal model delta sigma weight residual 1.468 1.384 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C4 7Q0 A 801 " pdb=" C5 7Q0 A 801 " ideal model delta sigma weight residual 1.455 1.388 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 30483 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 272 106.51 - 113.38: 34712 113.38 - 120.26: 11267 120.26 - 127.13: 8446 127.13 - 134.01: 139 Bond angle restraints: 54836 Sorted by residual: angle pdb=" C9 7Q0 E 801 " pdb=" C8 7Q0 E 801 " pdb=" N2 7Q0 E 801 " ideal model delta sigma weight residual 92.23 120.54 -28.31 3.00e+00 1.11e-01 8.90e+01 angle pdb=" C9 7Q0 A 801 " pdb=" C8 7Q0 A 801 " pdb=" N2 7Q0 A 801 " ideal model delta sigma weight residual 92.23 120.52 -28.29 3.00e+00 1.11e-01 8.89e+01 angle pdb=" C9 7Q0 G 801 " pdb=" C8 7Q0 G 801 " pdb=" N2 7Q0 G 801 " ideal model delta sigma weight residual 92.23 120.51 -28.28 3.00e+00 1.11e-01 8.89e+01 angle pdb=" C9 7Q0 C 801 " pdb=" C8 7Q0 C 801 " pdb=" N2 7Q0 C 801 " ideal model delta sigma weight residual 92.23 120.46 -28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" C7 7Q0 G 801 " pdb=" C8 7Q0 G 801 " pdb=" N2 7Q0 G 801 " ideal model delta sigma weight residual 145.97 119.72 26.25 3.00e+00 1.11e-01 7.66e+01 ... (remaining 54831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12358 17.90 - 35.81: 1287 35.81 - 53.71: 402 53.71 - 71.61: 95 71.61 - 89.52: 18 Dihedral angle restraints: 14160 sinusoidal: 7532 harmonic: 6628 Sorted by residual: dihedral pdb=" CA THR B 111 " pdb=" C THR B 111 " pdb=" N ASN B 112 " pdb=" CA ASN B 112 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR D 111 " pdb=" C THR D 111 " pdb=" N ASN D 112 " pdb=" CA ASN D 112 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR F 111 " pdb=" C THR F 111 " pdb=" N ASN F 112 " pdb=" CA ASN F 112 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1629 0.032 - 0.064: 491 0.064 - 0.096: 138 0.096 - 0.129: 29 0.129 - 0.161: 1 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA ILE F 101 " pdb=" N ILE F 101 " pdb=" C ILE F 101 " pdb=" CB ILE F 101 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR G 296 " pdb=" CA THR G 296 " pdb=" OG1 THR G 296 " pdb=" CG2 THR G 296 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB THR A 296 " pdb=" CA THR A 296 " pdb=" OG1 THR A 296 " pdb=" CG2 THR A 296 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 2285 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 560 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO E 561 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 561 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 561 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 560 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 561 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 561 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 561 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR G 298 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C THR G 298 " 0.023 2.00e-02 2.50e+03 pdb=" O THR G 298 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU G 299 " -0.008 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2017 2.18 - 2.79: 61858 2.79 - 3.39: 89358 3.39 - 4.00: 107268 4.00 - 4.60: 169032 Nonbonded interactions: 429533 Sorted by model distance: nonbonded pdb=" O ARG B 91 " pdb="HH11 ARG B 91 " model vdw 1.580 1.850 nonbonded pdb=" O ARG H 91 " pdb="HH11 ARG H 91 " model vdw 1.580 1.850 nonbonded pdb=" HH TYR A 95 " pdb=" OE1 GLU A 140 " model vdw 1.582 1.850 nonbonded pdb=" HH TYR G 95 " pdb=" OE1 GLU G 140 " model vdw 1.585 1.850 nonbonded pdb=" HH TYR E 95 " pdb=" OE1 GLU E 140 " model vdw 1.586 1.850 ... (remaining 429528 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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 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: 0.450 Extract box with map and model: 4.510 Check model and map are aligned: 0.460 Set scattering table: 0.250 Process input model: 97.910 Find NCS groups from input model: 1.280 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: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.005 0.086 15504 Z= 0.323 Angle : 0.920 28.308 20912 Z= 0.396 Chirality : 0.034 0.161 2288 Planarity : 0.003 0.050 2636 Dihedral : 17.021 89.519 5592 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.38 % Allowed : 23.36 % Favored : 76.26 % 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: 2.23 (0.20), residues: 1848 helix: 2.03 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 91 HIS 0.003 0.001 HIS C 228 PHE 0.017 0.001 PHE C 329 TYR 0.010 0.001 TYR G 74 ARG 0.003 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 315 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 89 ARG cc_start: 0.6289 (ptp90) cc_final: 0.5819 (ptm-80) REVERT: A 123 GLU cc_start: 0.7050 (tp30) cc_final: 0.6218 (tt0) REVERT: A 322 GLU cc_start: 0.7715 (tp30) cc_final: 0.7082 (mt-10) REVERT: A 334 ASN cc_start: 0.8055 (m-40) cc_final: 0.7818 (m110) REVERT: A 342 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6033 (m) REVERT: A 553 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7180 (tpt-90) REVERT: A 578 MET cc_start: 0.7306 (ptt) cc_final: 0.6969 (mmm) REVERT: B 73 MET cc_start: -0.1826 (mmm) cc_final: -0.2348 (ttm) REVERT: B 87 ARG cc_start: 0.5032 (tpp80) cc_final: 0.4823 (tmt-80) REVERT: B 106 LEU cc_start: 0.7011 (tp) cc_final: 0.6774 (tm) REVERT: B 107 ARG cc_start: 0.3520 (mtt90) cc_final: 0.3269 (tpp-160) REVERT: B 134 ASP cc_start: 0.5168 (p0) cc_final: 0.4149 (m-30) REVERT: C 89 ARG cc_start: 0.6196 (ptp90) cc_final: 0.5809 (ptm-80) REVERT: C 123 GLU cc_start: 0.7047 (tp30) cc_final: 0.6209 (tt0) REVERT: C 322 GLU cc_start: 0.7743 (tp30) cc_final: 0.7080 (mt-10) REVERT: C 334 ASN cc_start: 0.8006 (m-40) cc_final: 0.7791 (m110) REVERT: C 342 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.5993 (m) REVERT: D 73 MET cc_start: -0.2785 (mmt) cc_final: -0.3313 (ttm) REVERT: D 106 LEU cc_start: 0.6998 (tp) cc_final: 0.6789 (tm) REVERT: D 134 ASP cc_start: 0.5189 (p0) cc_final: 0.4157 (m-30) REVERT: D 142 PHE cc_start: 0.6645 (t80) cc_final: 0.6226 (t80) REVERT: D 146 MET cc_start: 0.6280 (mmm) cc_final: 0.5630 (mmm) REVERT: E 89 ARG cc_start: 0.6189 (ptp90) cc_final: 0.5769 (ptm-80) REVERT: E 123 GLU cc_start: 0.7109 (tp30) cc_final: 0.6259 (tt0) REVERT: E 152 CYS cc_start: 0.7820 (m) cc_final: 0.7378 (t) REVERT: E 322 GLU cc_start: 0.7714 (tp30) cc_final: 0.7055 (mt-10) REVERT: E 334 ASN cc_start: 0.8013 (m-40) cc_final: 0.7755 (m110) REVERT: E 342 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.5950 (m) REVERT: F 72 MET cc_start: -0.0260 (ptt) cc_final: -0.0462 (tmm) REVERT: F 73 MET cc_start: -0.1943 (mmm) cc_final: -0.2449 (ttm) REVERT: F 134 ASP cc_start: 0.5021 (p0) cc_final: 0.4004 (m-30) REVERT: F 142 PHE cc_start: 0.6706 (t80) cc_final: 0.6361 (t80) REVERT: F 146 MET cc_start: 0.6143 (mmm) cc_final: 0.5492 (mmm) REVERT: G 89 ARG cc_start: 0.6246 (ptp90) cc_final: 0.5681 (ptm-80) REVERT: G 123 GLU cc_start: 0.7091 (tp30) cc_final: 0.6250 (tt0) REVERT: G 152 CYS cc_start: 0.7893 (m) cc_final: 0.7408 (t) REVERT: G 322 GLU cc_start: 0.7697 (tp30) cc_final: 0.7226 (mt-10) REVERT: G 334 ASN cc_start: 0.7985 (m-40) cc_final: 0.7698 (m110) REVERT: G 342 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5947 (m) REVERT: G 553 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7037 (tpp80) REVERT: G 578 MET cc_start: 0.6921 (ptt) cc_final: 0.6586 (mmm) REVERT: H 72 MET cc_start: -0.0290 (ptt) cc_final: -0.0716 (tmm) REVERT: H 73 MET cc_start: -0.1817 (tpt) cc_final: -0.2833 (ttm) REVERT: H 87 ARG cc_start: 0.5257 (tpp80) cc_final: 0.4957 (tmt-80) REVERT: H 134 ASP cc_start: 0.5129 (p0) cc_final: 0.4089 (m-30) REVERT: H 142 PHE cc_start: 0.6759 (t80) cc_final: 0.6537 (t80) outliers start: 6 outliers final: 4 residues processed: 314 average time/residue: 2.6267 time to fit residues: 911.1281 Evaluate side-chains 255 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 167 optimal weight: 0.3980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15504 Z= 0.242 Angle : 0.590 13.639 20912 Z= 0.283 Chirality : 0.033 0.120 2288 Planarity : 0.003 0.033 2636 Dihedral : 5.038 56.125 2072 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.83 % Allowed : 23.93 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.20), residues: 1848 helix: 2.12 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.77 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 91 HIS 0.003 0.001 HIS G 96 PHE 0.013 0.001 PHE E 329 TYR 0.011 0.001 TYR G 74 ARG 0.003 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6207 (ptp90) cc_final: 0.5801 (ptm-80) REVERT: A 123 GLU cc_start: 0.6756 (tp30) cc_final: 0.6106 (tt0) REVERT: A 322 GLU cc_start: 0.7549 (tp30) cc_final: 0.7194 (mt-10) REVERT: A 334 ASN cc_start: 0.7893 (m-40) cc_final: 0.7636 (m110) REVERT: A 342 SER cc_start: 0.6282 (OUTLIER) cc_final: 0.5787 (m) REVERT: A 553 ARG cc_start: 0.7676 (mpt180) cc_final: 0.7089 (tpt-90) REVERT: A 578 MET cc_start: 0.7360 (ptt) cc_final: 0.6908 (mmm) REVERT: B 72 MET cc_start: 0.2011 (tmm) cc_final: 0.1540 (tmm) REVERT: B 73 MET cc_start: -0.2201 (mmm) cc_final: -0.2441 (ttm) REVERT: B 77 MET cc_start: 0.0435 (OUTLIER) cc_final: -0.1030 (mmt) REVERT: B 107 ARG cc_start: 0.3574 (mtt90) cc_final: 0.3325 (tpp-160) REVERT: B 134 ASP cc_start: 0.4833 (p0) cc_final: 0.3896 (m-30) REVERT: C 89 ARG cc_start: 0.6162 (ptp90) cc_final: 0.5809 (ptm-80) REVERT: C 123 GLU cc_start: 0.6752 (tp30) cc_final: 0.6098 (tt0) REVERT: C 214 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5694 (ptt180) REVERT: C 322 GLU cc_start: 0.7475 (tp30) cc_final: 0.7215 (mt-10) REVERT: C 334 ASN cc_start: 0.7856 (m-40) cc_final: 0.7611 (m110) REVERT: C 342 SER cc_start: 0.6258 (OUTLIER) cc_final: 0.5790 (m) REVERT: D 72 MET cc_start: 0.1890 (tmm) cc_final: 0.1553 (tmm) REVERT: D 73 MET cc_start: -0.2693 (mmt) cc_final: -0.3056 (ttm) REVERT: D 77 MET cc_start: 0.0652 (OUTLIER) cc_final: -0.0496 (mmt) REVERT: D 134 ASP cc_start: 0.5041 (p0) cc_final: 0.3984 (m-30) REVERT: D 142 PHE cc_start: 0.6774 (t80) cc_final: 0.6417 (t80) REVERT: D 146 MET cc_start: 0.6351 (mmm) cc_final: 0.5858 (mmm) REVERT: E 89 ARG cc_start: 0.6154 (ptp90) cc_final: 0.5774 (ptm-80) REVERT: E 123 GLU cc_start: 0.6842 (tp30) cc_final: 0.6190 (tt0) REVERT: E 152 CYS cc_start: 0.7778 (m) cc_final: 0.7238 (t) REVERT: E 176 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7175 (mp) REVERT: E 322 GLU cc_start: 0.7530 (tp30) cc_final: 0.7154 (mt-10) REVERT: E 334 ASN cc_start: 0.7941 (m-40) cc_final: 0.7667 (m110) REVERT: E 342 SER cc_start: 0.6119 (OUTLIER) cc_final: 0.5671 (m) REVERT: E 570 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7526 (tm-30) REVERT: F 72 MET cc_start: -0.0048 (ptt) cc_final: -0.0277 (tmm) REVERT: F 73 MET cc_start: -0.1961 (mmm) cc_final: -0.2503 (ttm) REVERT: F 77 MET cc_start: 0.0682 (OUTLIER) cc_final: 0.0300 (mtt) REVERT: F 134 ASP cc_start: 0.4856 (p0) cc_final: 0.3857 (t0) REVERT: F 142 PHE cc_start: 0.6776 (t80) cc_final: 0.6315 (t80) REVERT: F 145 MET cc_start: 0.5341 (ttp) cc_final: 0.5106 (ttp) REVERT: F 146 MET cc_start: 0.6291 (mmm) cc_final: 0.5752 (mmm) REVERT: G 89 ARG cc_start: 0.6354 (ptp90) cc_final: 0.5958 (ptm-80) REVERT: G 123 GLU cc_start: 0.6828 (tp30) cc_final: 0.6176 (tt0) REVERT: G 152 CYS cc_start: 0.7914 (m) cc_final: 0.7419 (t) REVERT: G 214 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.5657 (ptt180) REVERT: G 322 GLU cc_start: 0.7741 (tp30) cc_final: 0.7318 (mt-10) REVERT: G 334 ASN cc_start: 0.7971 (m-40) cc_final: 0.7664 (m110) REVERT: G 342 SER cc_start: 0.6328 (OUTLIER) cc_final: 0.5894 (m) REVERT: G 553 ARG cc_start: 0.7637 (mpt180) cc_final: 0.7296 (tmt170) REVERT: H 72 MET cc_start: -0.0326 (ptt) cc_final: -0.0680 (tmm) REVERT: H 73 MET cc_start: -0.1915 (tpt) cc_final: -0.2878 (ttm) REVERT: H 87 ARG cc_start: 0.5174 (tpp80) cc_final: 0.4933 (tmt-80) REVERT: H 134 ASP cc_start: 0.4912 (p0) cc_final: 0.3841 (t0) outliers start: 29 outliers final: 3 residues processed: 264 average time/residue: 2.4908 time to fit residues: 731.5384 Evaluate side-chains 247 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 342 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 180 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15504 Z= 0.424 Angle : 0.639 13.082 20912 Z= 0.317 Chirality : 0.037 0.150 2288 Planarity : 0.004 0.033 2636 Dihedral : 4.568 51.639 2066 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.90 % Allowed : 24.56 % Favored : 72.54 % 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: 2.14 (0.20), residues: 1848 helix: 1.95 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.67 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 91 HIS 0.004 0.001 HIS A 96 PHE 0.019 0.002 PHE E 329 TYR 0.017 0.001 TYR A 74 ARG 0.004 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6438 (ptp90) cc_final: 0.5940 (ptm-80) REVERT: A 123 GLU cc_start: 0.6716 (tp30) cc_final: 0.6052 (tt0) REVERT: A 322 GLU cc_start: 0.7546 (tp30) cc_final: 0.7126 (mt-10) REVERT: A 334 ASN cc_start: 0.7871 (m-40) cc_final: 0.7617 (m110) REVERT: A 342 SER cc_start: 0.6238 (OUTLIER) cc_final: 0.5813 (m) REVERT: A 544 CYS cc_start: 0.4961 (OUTLIER) cc_final: 0.3716 (m) REVERT: A 553 ARG cc_start: 0.7613 (mpt180) cc_final: 0.7000 (tpt-90) REVERT: A 578 MET cc_start: 0.6994 (ptt) cc_final: 0.6718 (mmm) REVERT: B 72 MET cc_start: 0.1689 (tmm) cc_final: 0.1318 (tmm) REVERT: B 107 ARG cc_start: 0.3754 (mtt90) cc_final: 0.3444 (tpp-160) REVERT: B 134 ASP cc_start: 0.5161 (p0) cc_final: 0.3875 (m-30) REVERT: C 89 ARG cc_start: 0.6425 (ptp90) cc_final: 0.5931 (ptm-80) REVERT: C 123 GLU cc_start: 0.6711 (tp30) cc_final: 0.6039 (tt0) REVERT: C 322 GLU cc_start: 0.7551 (tp30) cc_final: 0.7148 (mt-10) REVERT: C 334 ASN cc_start: 0.7855 (m-40) cc_final: 0.7582 (m110) REVERT: C 342 SER cc_start: 0.6331 (OUTLIER) cc_final: 0.5920 (m) REVERT: C 544 CYS cc_start: 0.4604 (OUTLIER) cc_final: 0.3491 (m) REVERT: D 72 MET cc_start: 0.2060 (tmm) cc_final: 0.1854 (tmm) REVERT: D 73 MET cc_start: -0.2897 (mmt) cc_final: -0.3124 (ttm) REVERT: D 77 MET cc_start: 0.0863 (mmt) cc_final: 0.0446 (mmt) REVERT: D 134 ASP cc_start: 0.5245 (p0) cc_final: 0.3992 (m-30) REVERT: D 142 PHE cc_start: 0.6800 (t80) cc_final: 0.6467 (t80) REVERT: D 145 MET cc_start: 0.5311 (ttp) cc_final: 0.5069 (ttp) REVERT: D 146 MET cc_start: 0.6279 (mmm) cc_final: 0.6032 (mmm) REVERT: E 89 ARG cc_start: 0.6414 (ptp90) cc_final: 0.5912 (ptm-80) REVERT: E 123 GLU cc_start: 0.6778 (tp30) cc_final: 0.6134 (tt0) REVERT: E 176 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7222 (mp) REVERT: E 322 GLU cc_start: 0.7567 (tp30) cc_final: 0.7123 (mt-10) REVERT: E 334 ASN cc_start: 0.7937 (m-40) cc_final: 0.7651 (m110) REVERT: E 342 SER cc_start: 0.6265 (OUTLIER) cc_final: 0.5875 (m) REVERT: E 544 CYS cc_start: 0.4750 (OUTLIER) cc_final: 0.3609 (m) REVERT: E 570 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7705 (tm-30) REVERT: F 72 MET cc_start: -0.0164 (ptt) cc_final: -0.0374 (tmm) REVERT: F 73 MET cc_start: -0.2225 (mmm) cc_final: -0.2541 (ttm) REVERT: F 134 ASP cc_start: 0.5069 (p0) cc_final: 0.3820 (m-30) REVERT: F 142 PHE cc_start: 0.6754 (t80) cc_final: 0.6372 (t80) REVERT: F 145 MET cc_start: 0.5378 (ttp) cc_final: 0.5107 (ttp) REVERT: F 146 MET cc_start: 0.6230 (mmm) cc_final: 0.5742 (mmm) REVERT: G 89 ARG cc_start: 0.6555 (ptp90) cc_final: 0.5982 (ptm-80) REVERT: G 123 GLU cc_start: 0.6752 (tp30) cc_final: 0.6105 (tt0) REVERT: G 322 GLU cc_start: 0.7698 (tp30) cc_final: 0.7287 (mt-10) REVERT: G 334 ASN cc_start: 0.7930 (m-40) cc_final: 0.7636 (m110) REVERT: G 342 SER cc_start: 0.6347 (OUTLIER) cc_final: 0.5978 (m) REVERT: G 544 CYS cc_start: 0.5201 (OUTLIER) cc_final: 0.3900 (m) REVERT: G 553 ARG cc_start: 0.7675 (mpt180) cc_final: 0.7167 (tpt-90) REVERT: H 72 MET cc_start: -0.0232 (ptt) cc_final: -0.0608 (tmm) REVERT: H 73 MET cc_start: -0.1809 (tpt) cc_final: -0.2804 (ttm) REVERT: H 134 ASP cc_start: 0.5091 (p0) cc_final: 0.3821 (m-30) outliers start: 46 outliers final: 19 residues processed: 257 average time/residue: 2.3411 time to fit residues: 673.3950 Evaluate side-chains 241 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15504 Z= 0.215 Angle : 0.585 13.560 20912 Z= 0.278 Chirality : 0.033 0.113 2288 Planarity : 0.003 0.032 2636 Dihedral : 4.291 51.021 2066 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.40 % Allowed : 24.56 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1848 helix: 2.16 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 269 HIS 0.003 0.001 HIS C 575 PHE 0.014 0.001 PHE C 329 TYR 0.009 0.001 TYR A 74 ARG 0.005 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 2.649 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 89 ARG cc_start: 0.6339 (ptp90) cc_final: 0.5915 (ptm-80) REVERT: A 123 GLU cc_start: 0.6708 (tp30) cc_final: 0.6033 (tt0) REVERT: A 322 GLU cc_start: 0.7484 (tp30) cc_final: 0.7139 (mt-10) REVERT: A 334 ASN cc_start: 0.7892 (m-40) cc_final: 0.7640 (m110) REVERT: A 342 SER cc_start: 0.6163 (OUTLIER) cc_final: 0.5659 (m) REVERT: A 544 CYS cc_start: 0.4949 (OUTLIER) cc_final: 0.3709 (m) REVERT: A 553 ARG cc_start: 0.7652 (mpt180) cc_final: 0.7005 (tpt-90) REVERT: A 578 MET cc_start: 0.6897 (ptt) cc_final: 0.6695 (mmm) REVERT: B 107 ARG cc_start: 0.3831 (mtt90) cc_final: 0.3616 (tpp-160) REVERT: B 125 MET cc_start: 0.6035 (tmm) cc_final: 0.5703 (tmm) REVERT: B 134 ASP cc_start: 0.5104 (p0) cc_final: 0.3813 (m-30) REVERT: C 89 ARG cc_start: 0.6359 (ptp90) cc_final: 0.5904 (ptm-80) REVERT: C 123 GLU cc_start: 0.6715 (tp30) cc_final: 0.6055 (tt0) REVERT: C 322 GLU cc_start: 0.7522 (tp30) cc_final: 0.7140 (mt-10) REVERT: C 334 ASN cc_start: 0.7866 (m-40) cc_final: 0.7594 (m110) REVERT: C 342 SER cc_start: 0.6285 (OUTLIER) cc_final: 0.5840 (m) REVERT: C 544 CYS cc_start: 0.4750 (OUTLIER) cc_final: 0.3512 (m) REVERT: C 553 ARG cc_start: 0.7699 (mpt180) cc_final: 0.7357 (tmt170) REVERT: D 72 MET cc_start: 0.1846 (tmm) cc_final: 0.1498 (tmm) REVERT: D 73 MET cc_start: -0.2785 (mmt) cc_final: -0.2999 (ttt) REVERT: D 77 MET cc_start: 0.0489 (OUTLIER) cc_final: -0.0530 (mmt) REVERT: D 134 ASP cc_start: 0.5170 (p0) cc_final: 0.3863 (m-30) REVERT: D 142 PHE cc_start: 0.6776 (t80) cc_final: 0.6393 (t80) REVERT: D 145 MET cc_start: 0.5373 (ttp) cc_final: 0.5169 (ttp) REVERT: D 146 MET cc_start: 0.6207 (mmm) cc_final: 0.5938 (mmm) REVERT: E 89 ARG cc_start: 0.6255 (ptp90) cc_final: 0.5757 (ptm-80) REVERT: E 123 GLU cc_start: 0.6762 (tp30) cc_final: 0.6099 (tt0) REVERT: E 176 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7181 (mp) REVERT: E 322 GLU cc_start: 0.7453 (tp30) cc_final: 0.7176 (mt-10) REVERT: E 334 ASN cc_start: 0.7942 (m-40) cc_final: 0.7651 (m110) REVERT: E 342 SER cc_start: 0.6266 (OUTLIER) cc_final: 0.5823 (m) REVERT: E 544 CYS cc_start: 0.4787 (OUTLIER) cc_final: 0.3590 (m) REVERT: F 73 MET cc_start: -0.2118 (mmm) cc_final: -0.2403 (ttm) REVERT: F 90 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7787 (t80) REVERT: F 134 ASP cc_start: 0.5009 (p0) cc_final: 0.3701 (m-30) REVERT: F 142 PHE cc_start: 0.6708 (t80) cc_final: 0.6363 (t80) REVERT: F 145 MET cc_start: 0.5318 (ttp) cc_final: 0.5091 (ttp) REVERT: F 146 MET cc_start: 0.6309 (mmm) cc_final: 0.5799 (mmm) REVERT: G 89 ARG cc_start: 0.6421 (ptp90) cc_final: 0.5929 (ptm-80) REVERT: G 123 GLU cc_start: 0.6747 (tp30) cc_final: 0.6070 (tt0) REVERT: G 322 GLU cc_start: 0.7651 (tp30) cc_final: 0.7240 (mt-10) REVERT: G 334 ASN cc_start: 0.7931 (m-40) cc_final: 0.7622 (m110) REVERT: G 342 SER cc_start: 0.6270 (OUTLIER) cc_final: 0.5843 (m) REVERT: G 544 CYS cc_start: 0.5179 (OUTLIER) cc_final: 0.3881 (m) REVERT: G 553 ARG cc_start: 0.7696 (mpt180) cc_final: 0.7154 (tpt-90) REVERT: H 72 MET cc_start: -0.0533 (ptt) cc_final: -0.0856 (tmm) REVERT: H 73 MET cc_start: -0.1832 (tpt) cc_final: -0.2791 (ttm) REVERT: H 134 ASP cc_start: 0.5040 (p0) cc_final: 0.3712 (m-30) outliers start: 38 outliers final: 12 residues processed: 251 average time/residue: 2.3222 time to fit residues: 653.4093 Evaluate side-chains 243 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 151 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 159 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 15504 Z= 0.491 Angle : 0.668 13.278 20912 Z= 0.338 Chirality : 0.039 0.159 2288 Planarity : 0.004 0.033 2636 Dihedral : 4.599 52.526 2066 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.29 % Allowed : 23.67 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1848 helix: 1.78 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 91 HIS 0.005 0.001 HIS G 96 PHE 0.026 0.002 PHE C 329 TYR 0.019 0.002 TYR G 74 ARG 0.007 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 217 time to evaluate : 2.582 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 89 ARG cc_start: 0.6475 (ptp90) cc_final: 0.6000 (ptm-80) REVERT: A 322 GLU cc_start: 0.7543 (tp30) cc_final: 0.7187 (mt-10) REVERT: A 342 SER cc_start: 0.6214 (OUTLIER) cc_final: 0.5795 (m) REVERT: A 544 CYS cc_start: 0.4899 (OUTLIER) cc_final: 0.3696 (m) REVERT: A 553 ARG cc_start: 0.7677 (mpt180) cc_final: 0.7013 (tpt-90) REVERT: A 578 MET cc_start: 0.6897 (ptt) cc_final: 0.6557 (mmm) REVERT: B 77 MET cc_start: 0.0771 (OUTLIER) cc_final: -0.0400 (mmt) REVERT: B 91 ARG cc_start: 0.8655 (ptm160) cc_final: 0.8230 (ptm160) REVERT: B 107 ARG cc_start: 0.3869 (mtt90) cc_final: 0.3582 (tpp-160) REVERT: C 89 ARG cc_start: 0.6488 (ptp90) cc_final: 0.5998 (ptm-80) REVERT: C 322 GLU cc_start: 0.7611 (tp30) cc_final: 0.7230 (mt-10) REVERT: C 342 SER cc_start: 0.6312 (OUTLIER) cc_final: 0.5914 (m) REVERT: C 544 CYS cc_start: 0.4644 (OUTLIER) cc_final: 0.3443 (m) REVERT: C 565 MET cc_start: 0.7493 (tpt) cc_final: 0.7061 (ptm) REVERT: D 73 MET cc_start: -0.2801 (mmt) cc_final: -0.3015 (ttt) REVERT: D 142 PHE cc_start: 0.6934 (t80) cc_final: 0.6685 (t80) REVERT: D 145 MET cc_start: 0.5385 (ttp) cc_final: 0.5123 (ttp) REVERT: D 146 MET cc_start: 0.6347 (mmm) cc_final: 0.6104 (mmm) REVERT: E 89 ARG cc_start: 0.6481 (ptp90) cc_final: 0.5974 (ptm-80) REVERT: E 176 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7272 (mp) REVERT: E 322 GLU cc_start: 0.7628 (tp30) cc_final: 0.7253 (mt-10) REVERT: E 342 SER cc_start: 0.6326 (OUTLIER) cc_final: 0.5922 (m) REVERT: E 544 CYS cc_start: 0.4797 (OUTLIER) cc_final: 0.3744 (m) REVERT: E 553 ARG cc_start: 0.7647 (mpt180) cc_final: 0.7337 (tmt170) REVERT: F 72 MET cc_start: 0.1761 (tmm) cc_final: 0.1398 (tmm) REVERT: F 90 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7573 (t80) REVERT: F 142 PHE cc_start: 0.6712 (t80) cc_final: 0.6401 (t80) REVERT: F 145 MET cc_start: 0.5447 (ttp) cc_final: 0.5233 (ttp) REVERT: F 146 MET cc_start: 0.6229 (mmm) cc_final: 0.5800 (mmm) REVERT: G 89 ARG cc_start: 0.6618 (ptp90) cc_final: 0.6045 (ptm-80) REVERT: G 176 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7088 (mp) REVERT: G 322 GLU cc_start: 0.7730 (tp30) cc_final: 0.7334 (mt-10) REVERT: G 342 SER cc_start: 0.6304 (OUTLIER) cc_final: 0.5927 (m) REVERT: G 544 CYS cc_start: 0.5212 (OUTLIER) cc_final: 0.4000 (m) REVERT: G 546 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5473 (mmp) REVERT: G 553 ARG cc_start: 0.7654 (mpt180) cc_final: 0.7121 (tpt-90) REVERT: H 72 MET cc_start: -0.0873 (ptt) cc_final: -0.1087 (tmm) REVERT: H 73 MET cc_start: -0.2067 (tpt) cc_final: -0.2985 (ttt) outliers start: 68 outliers final: 35 residues processed: 266 average time/residue: 2.2291 time to fit residues: 667.6849 Evaluate side-chains 256 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 91 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15504 Z= 0.177 Angle : 0.591 13.667 20912 Z= 0.279 Chirality : 0.033 0.124 2288 Planarity : 0.003 0.031 2636 Dihedral : 4.242 51.135 2066 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 25.00 % Favored : 72.16 % 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: 2.48 (0.20), residues: 1848 helix: 2.28 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 288 HIS 0.005 0.001 HIS D 108 PHE 0.012 0.001 PHE B 142 TYR 0.007 0.001 TYR A 74 ARG 0.004 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 219 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6250 (ptp90) cc_final: 0.5752 (ptm-80) REVERT: A 322 GLU cc_start: 0.7440 (tp30) cc_final: 0.7071 (mt-10) REVERT: A 342 SER cc_start: 0.6236 (OUTLIER) cc_final: 0.5670 (m) REVERT: A 544 CYS cc_start: 0.5004 (OUTLIER) cc_final: 0.3773 (m) REVERT: A 553 ARG cc_start: 0.7724 (mpt180) cc_final: 0.6906 (tpp80) REVERT: A 570 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 578 MET cc_start: 0.6929 (ptt) cc_final: 0.6661 (mmm) REVERT: C 89 ARG cc_start: 0.6239 (ptp90) cc_final: 0.5759 (ptm-80) REVERT: C 322 GLU cc_start: 0.7498 (tp30) cc_final: 0.7115 (mt-10) REVERT: C 342 SER cc_start: 0.6258 (OUTLIER) cc_final: 0.5789 (m) REVERT: C 544 CYS cc_start: 0.4749 (OUTLIER) cc_final: 0.3500 (m) REVERT: C 553 ARG cc_start: 0.7742 (mpt180) cc_final: 0.7121 (tpt-90) REVERT: D 72 MET cc_start: 0.1884 (tmm) cc_final: 0.1644 (tmm) REVERT: D 142 PHE cc_start: 0.6804 (t80) cc_final: 0.6550 (t80) REVERT: D 145 MET cc_start: 0.5467 (ttp) cc_final: 0.5265 (ttp) REVERT: D 146 MET cc_start: 0.6327 (mmm) cc_final: 0.5919 (mmm) REVERT: E 89 ARG cc_start: 0.6222 (ptp90) cc_final: 0.5745 (ptm-80) REVERT: E 176 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7147 (mp) REVERT: E 322 GLU cc_start: 0.7517 (tp30) cc_final: 0.7124 (mt-10) REVERT: E 334 ASN cc_start: 0.7921 (m-40) cc_final: 0.7601 (m110) REVERT: E 342 SER cc_start: 0.6241 (OUTLIER) cc_final: 0.5767 (m) REVERT: E 544 CYS cc_start: 0.4791 (OUTLIER) cc_final: 0.3623 (m) REVERT: E 553 ARG cc_start: 0.7646 (mpt180) cc_final: 0.7301 (tmt170) REVERT: F 86 ILE cc_start: 0.6449 (mm) cc_final: 0.6244 (OUTLIER) REVERT: F 90 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7517 (t80) REVERT: F 91 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8123 (ptm160) REVERT: F 142 PHE cc_start: 0.6677 (t80) cc_final: 0.6395 (t80) REVERT: F 146 MET cc_start: 0.6301 (mmm) cc_final: 0.5872 (mmm) REVERT: G 89 ARG cc_start: 0.6419 (ptp90) cc_final: 0.5839 (ptm-80) REVERT: G 176 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7051 (mp) REVERT: G 322 GLU cc_start: 0.7590 (tp30) cc_final: 0.7140 (mt-10) REVERT: G 334 ASN cc_start: 0.7919 (m-40) cc_final: 0.7605 (m110) REVERT: G 342 SER cc_start: 0.6341 (OUTLIER) cc_final: 0.5887 (m) REVERT: G 544 CYS cc_start: 0.5112 (OUTLIER) cc_final: 0.3939 (m) REVERT: G 546 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.5518 (mmp) REVERT: G 553 ARG cc_start: 0.7625 (mpt180) cc_final: 0.7096 (tpt-90) REVERT: H 72 MET cc_start: -0.0617 (OUTLIER) cc_final: -0.0894 (tmm) REVERT: H 73 MET cc_start: -0.2154 (tpt) cc_final: -0.3095 (ttt) REVERT: H 77 MET cc_start: 0.0479 (OUTLIER) cc_final: -0.0722 (mmt) REVERT: H 91 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7929 (ptm160) outliers start: 45 outliers final: 21 residues processed: 246 average time/residue: 2.2977 time to fit residues: 633.9458 Evaluate side-chains 245 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 91 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 130 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 40.0000 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15504 Z= 0.388 Angle : 0.639 13.095 20912 Z= 0.315 Chirality : 0.036 0.143 2288 Planarity : 0.004 0.033 2636 Dihedral : 4.452 52.266 2066 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.54 % Allowed : 25.51 % Favored : 70.96 % 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: 2.27 (0.19), residues: 1848 helix: 2.14 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.09 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 91 HIS 0.005 0.001 HIS G 96 PHE 0.021 0.001 PHE A 329 TYR 0.015 0.001 TYR G 74 ARG 0.003 0.000 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 202 time to evaluate : 2.193 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 89 ARG cc_start: 0.6444 (ptp90) cc_final: 0.5907 (ptm-80) REVERT: A 322 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 342 SER cc_start: 0.6136 (OUTLIER) cc_final: 0.5640 (m) REVERT: A 544 CYS cc_start: 0.4936 (OUTLIER) cc_final: 0.3732 (m) REVERT: A 553 ARG cc_start: 0.7748 (mpt180) cc_final: 0.7098 (tpt-90) REVERT: A 578 MET cc_start: 0.6917 (ptt) cc_final: 0.6562 (mmm) REVERT: B 91 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8409 (ptp-170) REVERT: C 89 ARG cc_start: 0.6418 (ptp90) cc_final: 0.5907 (ptm-80) REVERT: C 322 GLU cc_start: 0.7602 (tp30) cc_final: 0.7244 (mt-10) REVERT: C 342 SER cc_start: 0.6270 (OUTLIER) cc_final: 0.5828 (m) REVERT: C 544 CYS cc_start: 0.4721 (OUTLIER) cc_final: 0.3453 (m) REVERT: C 553 ARG cc_start: 0.7720 (mpt180) cc_final: 0.7351 (tmt170) REVERT: D 90 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7758 (t80) REVERT: D 113 LEU cc_start: 0.5944 (mp) cc_final: 0.5188 (tt) REVERT: D 146 MET cc_start: 0.6312 (mmm) cc_final: 0.6094 (mmm) REVERT: E 89 ARG cc_start: 0.6427 (ptp90) cc_final: 0.5898 (ptm-80) REVERT: E 176 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7189 (mp) REVERT: E 322 GLU cc_start: 0.7626 (tp30) cc_final: 0.7260 (mt-10) REVERT: E 342 SER cc_start: 0.6300 (OUTLIER) cc_final: 0.5876 (m) REVERT: E 544 CYS cc_start: 0.4802 (OUTLIER) cc_final: 0.3606 (m) REVERT: E 553 ARG cc_start: 0.7676 (mpt180) cc_final: 0.7329 (tmt170) REVERT: E 565 MET cc_start: 0.7351 (tpt) cc_final: 0.7113 (ptm) REVERT: F 90 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7456 (t80) REVERT: F 91 ARG cc_start: 0.8504 (ptm160) cc_final: 0.8152 (ptm160) REVERT: F 142 PHE cc_start: 0.6703 (t80) cc_final: 0.6352 (t80) REVERT: F 145 MET cc_start: 0.5234 (ttp) cc_final: 0.4981 (ttp) REVERT: F 146 MET cc_start: 0.6161 (mmm) cc_final: 0.5938 (mmm) REVERT: G 89 ARG cc_start: 0.6551 (ptp90) cc_final: 0.6015 (ptm-80) REVERT: G 176 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7082 (mp) REVERT: G 322 GLU cc_start: 0.7617 (tp30) cc_final: 0.7222 (mt-10) REVERT: G 334 ASN cc_start: 0.7822 (m-40) cc_final: 0.7512 (m110) REVERT: G 342 SER cc_start: 0.6290 (OUTLIER) cc_final: 0.5837 (m) REVERT: G 544 CYS cc_start: 0.5079 (OUTLIER) cc_final: 0.3953 (m) REVERT: G 546 MET cc_start: 0.5674 (OUTLIER) cc_final: 0.5461 (mmp) REVERT: G 553 ARG cc_start: 0.7649 (mpt180) cc_final: 0.7101 (tpt-90) REVERT: H 73 MET cc_start: -0.2235 (tpt) cc_final: -0.3132 (ttt) REVERT: H 90 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7786 (t80) REVERT: H 91 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8019 (ptm160) outliers start: 56 outliers final: 29 residues processed: 238 average time/residue: 2.4295 time to fit residues: 654.6506 Evaluate side-chains 245 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 570 GLN Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 91 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 40.0000 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15504 Z= 0.244 Angle : 0.617 13.561 20912 Z= 0.294 Chirality : 0.033 0.115 2288 Planarity : 0.003 0.033 2636 Dihedral : 4.335 51.846 2066 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.97 % Allowed : 25.82 % Favored : 71.21 % 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: 2.47 (0.20), residues: 1848 helix: 2.26 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 269 HIS 0.004 0.001 HIS H 108 PHE 0.015 0.001 PHE A 329 TYR 0.010 0.001 TYR A 74 ARG 0.003 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 211 time to evaluate : 2.505 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 89 ARG cc_start: 0.6366 (ptp90) cc_final: 0.5844 (ptm-80) REVERT: A 322 GLU cc_start: 0.7457 (tp30) cc_final: 0.7094 (mt-10) REVERT: A 342 SER cc_start: 0.6151 (OUTLIER) cc_final: 0.5662 (m) REVERT: A 544 CYS cc_start: 0.4974 (OUTLIER) cc_final: 0.3732 (m) REVERT: A 553 ARG cc_start: 0.7752 (mpt180) cc_final: 0.7087 (tpt-90) REVERT: A 578 MET cc_start: 0.6913 (ptt) cc_final: 0.6586 (mmm) REVERT: C 89 ARG cc_start: 0.6361 (ptp90) cc_final: 0.5909 (ptm-80) REVERT: C 322 GLU cc_start: 0.7597 (tp30) cc_final: 0.7201 (mt-10) REVERT: C 342 SER cc_start: 0.6307 (OUTLIER) cc_final: 0.5869 (m) REVERT: C 544 CYS cc_start: 0.4900 (OUTLIER) cc_final: 0.3505 (m) REVERT: C 553 ARG cc_start: 0.7723 (mpt180) cc_final: 0.7338 (tmt170) REVERT: D 90 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (t80) REVERT: D 142 PHE cc_start: 0.7036 (t80) cc_final: 0.6746 (t80) REVERT: D 146 MET cc_start: 0.6162 (mmm) cc_final: 0.5896 (mmm) REVERT: E 89 ARG cc_start: 0.6345 (ptp90) cc_final: 0.5884 (ptm-80) REVERT: E 176 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7104 (mp) REVERT: E 322 GLU cc_start: 0.7592 (tp30) cc_final: 0.7210 (mt-10) REVERT: E 342 SER cc_start: 0.6263 (OUTLIER) cc_final: 0.5772 (m) REVERT: E 544 CYS cc_start: 0.4837 (OUTLIER) cc_final: 0.3601 (m) REVERT: E 553 ARG cc_start: 0.7684 (mpt180) cc_final: 0.7319 (tmt170) REVERT: F 90 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7421 (t80) REVERT: F 91 ARG cc_start: 0.8491 (ptm160) cc_final: 0.8139 (ptm160) REVERT: F 142 PHE cc_start: 0.6711 (t80) cc_final: 0.6346 (t80) REVERT: F 145 MET cc_start: 0.5270 (ttp) cc_final: 0.5055 (ttp) REVERT: F 146 MET cc_start: 0.6122 (mmm) cc_final: 0.5898 (mmm) REVERT: G 89 ARG cc_start: 0.6426 (ptp90) cc_final: 0.5889 (ptm-80) REVERT: G 176 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7028 (mp) REVERT: G 322 GLU cc_start: 0.7585 (tp30) cc_final: 0.7134 (mt-10) REVERT: G 342 SER cc_start: 0.6298 (OUTLIER) cc_final: 0.5824 (m) REVERT: G 544 CYS cc_start: 0.5238 (OUTLIER) cc_final: 0.3962 (m) REVERT: G 553 ARG cc_start: 0.7654 (mpt180) cc_final: 0.7096 (tpt-90) REVERT: H 72 MET cc_start: 0.1779 (tmm) cc_final: 0.1546 (tmm) REVERT: H 73 MET cc_start: -0.2366 (tpt) cc_final: -0.3147 (ttt) REVERT: H 90 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7741 (t80) REVERT: H 91 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8035 (ptm160) REVERT: H 113 LEU cc_start: 0.6041 (mp) cc_final: 0.5330 (tt) outliers start: 47 outliers final: 24 residues processed: 240 average time/residue: 2.2090 time to fit residues: 595.7403 Evaluate side-chains 244 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 91 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15504 Z= 0.342 Angle : 0.644 13.371 20912 Z= 0.312 Chirality : 0.035 0.134 2288 Planarity : 0.004 0.034 2636 Dihedral : 4.430 52.402 2066 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.09 % Allowed : 26.14 % Favored : 70.77 % 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: 2.36 (0.20), residues: 1848 helix: 2.21 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 91 HIS 0.004 0.001 HIS G 96 PHE 0.020 0.001 PHE A 329 TYR 0.013 0.001 TYR A 74 ARG 0.003 0.000 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 2.196 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: A 89 ARG cc_start: 0.6398 (ptp90) cc_final: 0.5905 (ptm-80) REVERT: A 322 GLU cc_start: 0.7523 (tp30) cc_final: 0.7167 (mt-10) REVERT: A 342 SER cc_start: 0.6165 (OUTLIER) cc_final: 0.5693 (m) REVERT: A 544 CYS cc_start: 0.5160 (OUTLIER) cc_final: 0.3809 (m) REVERT: A 553 ARG cc_start: 0.7764 (mpt180) cc_final: 0.6970 (tpp80) REVERT: A 570 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 578 MET cc_start: 0.6878 (ptt) cc_final: 0.6504 (mmm) REVERT: B 77 MET cc_start: 0.0443 (OUTLIER) cc_final: -0.0607 (mmt) REVERT: B 91 ARG cc_start: 0.8612 (ptm160) cc_final: 0.8372 (ptp-170) REVERT: C 89 ARG cc_start: 0.6402 (ptp90) cc_final: 0.5920 (ptm-80) REVERT: C 176 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7482 (tt) REVERT: C 322 GLU cc_start: 0.7596 (tp30) cc_final: 0.7235 (mt-10) REVERT: C 342 SER cc_start: 0.6320 (OUTLIER) cc_final: 0.5899 (m) REVERT: C 544 CYS cc_start: 0.4889 (OUTLIER) cc_final: 0.3485 (m) REVERT: C 553 ARG cc_start: 0.7705 (mpt180) cc_final: 0.7330 (tmt170) REVERT: D 90 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7511 (t80) REVERT: D 142 PHE cc_start: 0.7006 (t80) cc_final: 0.6652 (t80) REVERT: D 145 MET cc_start: 0.5221 (ttp) cc_final: 0.4917 (ttp) REVERT: D 146 MET cc_start: 0.6305 (mmm) cc_final: 0.6030 (mmm) REVERT: E 89 ARG cc_start: 0.6384 (ptp90) cc_final: 0.5895 (ptm-80) REVERT: E 176 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7120 (mp) REVERT: E 322 GLU cc_start: 0.7572 (tp30) cc_final: 0.7214 (mt-10) REVERT: E 342 SER cc_start: 0.6321 (OUTLIER) cc_final: 0.5859 (m) REVERT: E 544 CYS cc_start: 0.4974 (OUTLIER) cc_final: 0.3689 (m) REVERT: E 553 ARG cc_start: 0.7731 (mpt180) cc_final: 0.7367 (tmt170) REVERT: F 90 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7328 (t80) REVERT: F 91 ARG cc_start: 0.8557 (ptm160) cc_final: 0.8182 (ptm160) REVERT: F 142 PHE cc_start: 0.6701 (t80) cc_final: 0.6372 (t80) REVERT: F 145 MET cc_start: 0.5377 (ttp) cc_final: 0.5175 (ttp) REVERT: F 146 MET cc_start: 0.6128 (mmm) cc_final: 0.5896 (mmm) REVERT: G 89 ARG cc_start: 0.6552 (ptp90) cc_final: 0.6016 (ptm-80) REVERT: G 176 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7061 (mp) REVERT: G 322 GLU cc_start: 0.7599 (tp30) cc_final: 0.7204 (mt-10) REVERT: G 342 SER cc_start: 0.6273 (OUTLIER) cc_final: 0.5801 (m) REVERT: G 544 CYS cc_start: 0.5162 (OUTLIER) cc_final: 0.3861 (m) REVERT: G 553 ARG cc_start: 0.7633 (mpt180) cc_final: 0.7083 (tpt-90) REVERT: H 72 MET cc_start: 0.1583 (tmm) cc_final: 0.1215 (tmm) REVERT: H 73 MET cc_start: -0.2451 (tpt) cc_final: -0.3232 (ttt) REVERT: H 90 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7561 (t80) REVERT: H 91 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8013 (ptm160) outliers start: 49 outliers final: 27 residues processed: 235 average time/residue: 2.3274 time to fit residues: 612.4186 Evaluate side-chains 245 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 202 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 91 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15504 Z= 0.231 Angle : 0.623 13.520 20912 Z= 0.294 Chirality : 0.033 0.116 2288 Planarity : 0.003 0.034 2636 Dihedral : 4.306 52.080 2066 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.78 % Allowed : 26.58 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.20), residues: 1848 helix: 2.36 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.01 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 344 HIS 0.003 0.001 HIS F 108 PHE 0.014 0.001 PHE A 329 TYR 0.010 0.001 TYR A 74 ARG 0.005 0.000 ARG C 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 2.153 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: A 89 ARG cc_start: 0.6343 (ptp90) cc_final: 0.5887 (ptm-80) REVERT: A 322 GLU cc_start: 0.7420 (tp30) cc_final: 0.7053 (mt-10) REVERT: A 342 SER cc_start: 0.6156 (OUTLIER) cc_final: 0.5666 (m) REVERT: A 544 CYS cc_start: 0.5072 (OUTLIER) cc_final: 0.3696 (m) REVERT: A 553 ARG cc_start: 0.7729 (mpt180) cc_final: 0.6938 (tpp80) REVERT: A 570 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 578 MET cc_start: 0.6868 (ptt) cc_final: 0.6505 (mmm) REVERT: B 91 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8349 (ptp-170) REVERT: C 89 ARG cc_start: 0.6335 (ptp90) cc_final: 0.5892 (ptm-80) REVERT: C 322 GLU cc_start: 0.7583 (tp30) cc_final: 0.7207 (mt-10) REVERT: C 342 SER cc_start: 0.6322 (OUTLIER) cc_final: 0.5896 (m) REVERT: C 544 CYS cc_start: 0.4899 (OUTLIER) cc_final: 0.3363 (m) REVERT: C 553 ARG cc_start: 0.7707 (mpt180) cc_final: 0.7321 (tmt170) REVERT: D 90 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7455 (t80) REVERT: D 142 PHE cc_start: 0.6974 (t80) cc_final: 0.6629 (t80) REVERT: D 145 MET cc_start: 0.5258 (ttp) cc_final: 0.4975 (ttp) REVERT: D 146 MET cc_start: 0.6293 (mmm) cc_final: 0.6007 (mmm) REVERT: E 89 ARG cc_start: 0.6331 (ptp90) cc_final: 0.5875 (ptm-80) REVERT: E 176 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7125 (mp) REVERT: E 322 GLU cc_start: 0.7493 (tp30) cc_final: 0.7119 (mt-10) REVERT: E 334 ASN cc_start: 0.7904 (m-40) cc_final: 0.7586 (m110) REVERT: E 342 SER cc_start: 0.6309 (OUTLIER) cc_final: 0.5832 (m) REVERT: E 544 CYS cc_start: 0.4966 (OUTLIER) cc_final: 0.3666 (m) REVERT: E 553 ARG cc_start: 0.7753 (mpt180) cc_final: 0.7381 (tmt170) REVERT: F 90 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7322 (t80) REVERT: F 91 ARG cc_start: 0.8523 (ptm160) cc_final: 0.8139 (ptm160) REVERT: F 142 PHE cc_start: 0.6721 (t80) cc_final: 0.6379 (t80) REVERT: F 145 MET cc_start: 0.5357 (ttp) cc_final: 0.5149 (ttp) REVERT: F 146 MET cc_start: 0.6110 (mmm) cc_final: 0.5886 (mmm) REVERT: G 89 ARG cc_start: 0.6405 (ptp90) cc_final: 0.5890 (ptm-80) REVERT: G 176 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7044 (mp) REVERT: G 322 GLU cc_start: 0.7581 (tp30) cc_final: 0.7133 (mt-10) REVERT: G 342 SER cc_start: 0.6266 (OUTLIER) cc_final: 0.5779 (m) REVERT: G 544 CYS cc_start: 0.5151 (OUTLIER) cc_final: 0.3749 (m) REVERT: G 553 ARG cc_start: 0.7636 (mpt180) cc_final: 0.7074 (tpt-90) REVERT: H 72 MET cc_start: 0.1714 (tmm) cc_final: 0.1382 (tmm) REVERT: H 73 MET cc_start: -0.2456 (tpt) cc_final: -0.3238 (ttt) REVERT: H 90 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7451 (t80) REVERT: H 91 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7996 (ptm160) outliers start: 44 outliers final: 25 residues processed: 236 average time/residue: 2.2431 time to fit residues: 600.9728 Evaluate side-chains 246 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 91 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 128 optimal weight: 30.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.223673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148276 restraints weight = 56215.238| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 4.05 r_work: 0.3299 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15504 Z= 0.246 Angle : 0.627 13.488 20912 Z= 0.297 Chirality : 0.033 0.117 2288 Planarity : 0.003 0.035 2636 Dihedral : 4.297 52.210 2066 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.71 % Allowed : 26.83 % Favored : 70.45 % 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: 2.67 (0.20), residues: 1848 helix: 2.42 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 91 HIS 0.005 0.001 HIS E 575 PHE 0.015 0.001 PHE A 329 TYR 0.010 0.001 TYR E 74 ARG 0.004 0.000 ARG G 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10725.09 seconds wall clock time: 188 minutes 0.77 seconds (11280.77 seconds total)