Starting phenix.real_space_refine on Thu Feb 15 00:52:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1s_16382/02_2024/8c1s_16382_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1s_16382/02_2024/8c1s_16382.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1s_16382/02_2024/8c1s_16382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1s_16382/02_2024/8c1s_16382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1s_16382/02_2024/8c1s_16382_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1s_16382/02_2024/8c1s_16382_neut_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 ------------------------------------------------------------------------------- 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= 0.001 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 72 5.16 5 C 7136 2.51 5 N 1638 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 627": "OE1" <-> "OE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ARG 209": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10668 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1173 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 151, 1173 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1180 Chain: "B" Number of atoms: 1204 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1182 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 154, 1182 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 1189 Chain: "C" Number of atoms: 1169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1147 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 149, 1147 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1152 Chain: "D" Number of atoms: 1217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1195 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 155, 1195 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1202 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1381 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1379 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'PLM': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'PLM': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE B 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 574 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE C 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 574 " occ=0.50 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 8.28, per 1000 atoms: 0.78 Number of scatterers: 10668 At special positions: 0 Unit cell: (96.642, 97.468, 96.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 4 15.00 O 1818 8.00 N 1638 7.00 C 7136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.05 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.07 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 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: 4.38 Conformation dependent library (CDL) restraints added in 2.8 seconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 5 sheets defined 64.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 544 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 628 Processing helix chain 'A' and resid 789 through 819 removed outlier: 3.542A pdb=" N ALA A 793 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY A 794 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 542 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 793 through 822 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 545 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 628 Processing helix chain 'C' and resid 793 through 820 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.582A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 822 Processing helix chain 'E' and resid 8 through 29 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 134 through 161 removed outlier: 3.603A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 209 Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.639A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.899A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 Processing helix chain 'F' and resid 178 through 209 Processing helix chain 'G' and resid 8 through 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 126 removed outlier: 4.083A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 removed outlier: 3.541A pdb=" N GLY G 139 " --> pdb=" O ILE G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 209 removed outlier: 3.623A pdb=" N LEU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 29 removed outlier: 4.049A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 106 through 126 removed outlier: 4.302A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 160 Processing helix chain 'H' and resid 178 through 209 removed outlier: 3.891A pdb=" N ARG H 209 " --> pdb=" O HIS H 205 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= B, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.887A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 174 through 176 Processing sheet with id= D, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= E, first strand: chain 'H' and resid 65 through 67 715 hydrogen bonds defined for protein. 2053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1578 1.31 - 1.44: 3310 1.44 - 1.58: 5908 1.58 - 1.71: 9 1.71 - 1.84: 111 Bond restraints: 10916 Sorted by residual: bond pdb=" CA SER B 544 " pdb=" CB SER B 544 " ideal model delta sigma weight residual 1.533 1.441 0.092 1.60e-02 3.91e+03 3.28e+01 bond pdb=" CG MET B 585 " pdb=" SD MET B 585 " ideal model delta sigma weight residual 1.803 1.678 0.125 2.50e-02 1.60e+03 2.48e+01 bond pdb=" CA SER D 592 " pdb=" CB SER D 592 " ideal model delta sigma weight residual 1.536 1.460 0.076 1.83e-02 2.99e+03 1.74e+01 bond pdb=" C LEU D 581 " pdb=" N GLY D 582 " ideal model delta sigma weight residual 1.335 1.286 0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" C GLN G 207 " pdb=" O GLN G 207 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.17e-02 7.31e+03 1.57e+01 ... (remaining 10911 not shown) Histogram of bond angle deviations from ideal: 95.88 - 103.61: 95 103.61 - 111.34: 3949 111.34 - 119.06: 4829 119.06 - 126.79: 5677 126.79 - 134.52: 144 Bond angle restraints: 14694 Sorted by residual: angle pdb=" N ASN B 575 " pdb=" CA ASN B 575 " pdb=" C ASN B 575 " ideal model delta sigma weight residual 113.50 103.41 10.09 1.23e+00 6.61e-01 6.73e+01 angle pdb=" O GLN C 587 " pdb=" C GLN C 587 " pdb=" N GLY C 588 " ideal model delta sigma weight residual 120.83 125.68 -4.85 7.40e-01 1.83e+00 4.30e+01 angle pdb=" O GLN G 207 " pdb=" C GLN G 207 " pdb=" N LEU G 208 " ideal model delta sigma weight residual 122.12 115.54 6.58 1.06e+00 8.90e-01 3.85e+01 angle pdb=" N PRO A 548 " pdb=" CA PRO A 548 " pdb=" CB PRO A 548 " ideal model delta sigma weight residual 103.25 96.78 6.47 1.05e+00 9.07e-01 3.80e+01 angle pdb=" C GLN C 587 " pdb=" CA GLN C 587 " pdb=" CB GLN C 587 " ideal model delta sigma weight residual 115.27 103.01 12.26 2.00e+00 2.50e-01 3.75e+01 ... (remaining 14689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 5954 29.36 - 58.72: 302 58.72 - 88.07: 38 88.07 - 117.43: 8 117.43 - 146.79: 2 Dihedral angle restraints: 6304 sinusoidal: 2514 harmonic: 3790 Sorted by residual: dihedral pdb=" CD ARG G 204 " pdb=" NE ARG G 204 " pdb=" CZ ARG G 204 " pdb=" NH1 ARG G 204 " ideal model delta sinusoidal sigma weight residual 0.00 82.28 -82.28 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 28.27 64.73 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 42.48 50.52 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 6301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 980 0.067 - 0.135: 477 0.135 - 0.202: 140 0.202 - 0.270: 26 0.270 - 0.337: 5 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CB ILE F 157 " pdb=" CA ILE F 157 " pdb=" CG1 ILE F 157 " pdb=" CG2 ILE F 157 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA SER D 615 " pdb=" N SER D 615 " pdb=" C SER D 615 " pdb=" CB SER D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PHE F 107 " pdb=" N PHE F 107 " pdb=" C PHE F 107 " pdb=" CB PHE F 107 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1625 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 204 " 1.040 9.50e-02 1.11e+02 4.67e-01 1.39e+02 pdb=" NE ARG G 204 " -0.080 2.00e-02 2.50e+03 pdb=" CZ ARG G 204 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG G 204 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 204 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 209 " -0.916 9.50e-02 1.11e+02 4.12e-01 1.13e+02 pdb=" NE ARG H 209 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG H 209 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG H 209 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG H 209 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 586 " -0.833 9.50e-02 1.11e+02 3.75e-01 9.49e+01 pdb=" NE ARG C 586 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 586 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 586 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 586 " -0.042 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1910 2.77 - 3.30: 10955 3.30 - 3.83: 17853 3.83 - 4.37: 20431 4.37 - 4.90: 36001 Nonbonded interactions: 87150 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.234 2.440 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.249 3.040 nonbonded pdb=" O ASP E 31 " pdb=" O SER E 61 " model vdw 2.313 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.338 2.520 nonbonded pdb=" N MET E 58 " pdb=" OE2 GLU E 70 " model vdw 2.339 2.520 ... (remaining 87145 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' and (resid 506 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 549 or resid 571 t \ hrough 573 or resid 575 through 622 or resid 624 through 626 or (resid 627 and ( \ name N or name CA or name C or name O or name CB )) or resid 628 through 633 or \ (resid 634 through 784 and (name N or name CA or name C or name O or name CB )) \ or resid 785 through 812 or (resid 813 and (name N or name CA or name C or name \ O or name CB )) or resid 814 through 818 or (resid 819 through 823 and (name N o \ r name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 506 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 549 or resid 5 \ 71 through 573 or resid 575 or (resid 576 and (name N or name CA or name C or na \ me O or name CB )) or resid 577 through 622 or resid 624 through 634 or (resid 7 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 785 through \ 823)) selection = (chain 'C' and (resid 506 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 622 or resid 624 \ through 626 or (resid 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 through 633 or (resid 634 through 784 and (name N or name CA or \ name C or name O or name CB )) or resid 785 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 818 or (resi \ d 819 through 823 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 506 through 507 or (resid 508 through 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 549 or resid 5 \ 71 through 573 or resid 575 or (resid 576 and (name N or name CA or name C or na \ me O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 6 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 628 through \ 634 or (resid 784 and (name N or name CA or name C or name O or name CB )) or r \ esid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 208 or (resid 209 through \ 210 and (name N or name CA or name C or name O or name CB )))) } 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=0.50 max=1.00 mean=0.99 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.240 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 35.360 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.012 0.125 10916 Z= 0.754 Angle : 1.285 12.255 14694 Z= 0.810 Chirality : 0.084 0.337 1628 Planarity : 0.025 0.467 1760 Dihedral : 17.433 146.791 3852 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.90 % Rotamer: Outliers : 1.87 % Allowed : 3.82 % Favored : 94.31 % 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: 1.35 (0.23), residues: 1286 helix: 2.11 (0.16), residues: 921 sheet: -0.09 (1.96), residues: 10 loop : -2.53 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.013 TRP B 578 HIS 0.016 0.005 HIS F 205 PHE 0.078 0.011 PHE A 571 TYR 0.058 0.010 TYR H 35 ARG 0.058 0.005 ARG H 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 LYS cc_start: 0.7861 (tttm) cc_final: 0.7546 (tmmt) REVERT: B 594 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8061 (mtm-85) REVERT: C 594 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8383 (mtp-110) REVERT: C 807 MET cc_start: 0.8925 (mtm) cc_final: 0.8538 (mtm) REVERT: D 594 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8587 (mtm110) REVERT: E 122 ILE cc_start: 0.7947 (mm) cc_final: 0.7703 (tt) REVERT: E 199 HIS cc_start: 0.7571 (t-90) cc_final: 0.7331 (t-90) REVERT: F 61 SER cc_start: 0.8883 (t) cc_final: 0.8644 (m) REVERT: F 65 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7391 (mtp85) REVERT: F 204 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7717 (mpt-90) REVERT: F 207 GLN cc_start: 0.7437 (tt0) cc_final: 0.7185 (tm-30) REVERT: H 56 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7086 (mm-30) REVERT: H 65 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7245 (mtm-85) REVERT: H 99 ARG cc_start: 0.7975 (mmt180) cc_final: 0.7529 (mtt180) outliers start: 20 outliers final: 5 residues processed: 214 average time/residue: 1.3440 time to fit residues: 308.1945 Evaluate side-chains 172 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 204 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS G 133 ASN H 79 GLN H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10916 Z= 0.203 Angle : 0.532 7.058 14694 Z= 0.287 Chirality : 0.039 0.212 1628 Planarity : 0.005 0.040 1760 Dihedral : 13.862 110.347 1725 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.52 % Allowed : 11.57 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1286 helix: 3.01 (0.17), residues: 919 sheet: -0.22 (1.83), residues: 10 loop : -2.09 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS H 60 PHE 0.018 0.001 PHE G 73 TYR 0.014 0.001 TYR H 174 ARG 0.010 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 589 CYS cc_start: 0.7994 (t) cc_final: 0.7477 (p) REVERT: B 594 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8120 (mtm-85) REVERT: B 626 VAL cc_start: 0.8854 (m) cc_final: 0.8652 (p) REVERT: C 594 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8356 (mtp-110) REVERT: D 594 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8503 (mtm110) REVERT: E 73 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6238 (p90) REVERT: F 11 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7973 (tm) REVERT: F 65 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7450 (mtp85) REVERT: G 131 ARG cc_start: 0.6636 (tpp80) cc_final: 0.6327 (tpp80) REVERT: G 205 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6836 (t-90) REVERT: H 99 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7377 (tpp80) outliers start: 27 outliers final: 12 residues processed: 192 average time/residue: 1.3378 time to fit residues: 274.7395 Evaluate side-chains 182 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 10916 Z= 0.433 Angle : 0.620 7.846 14694 Z= 0.331 Chirality : 0.044 0.209 1628 Planarity : 0.005 0.041 1760 Dihedral : 13.316 93.306 1714 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.89 % Allowed : 14.55 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1286 helix: 2.67 (0.17), residues: 921 sheet: -1.87 (1.41), residues: 12 loop : -2.11 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 578 HIS 0.004 0.001 HIS F 60 PHE 0.024 0.002 PHE E 127 TYR 0.013 0.002 TYR D 523 ARG 0.008 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: C 594 ARG cc_start: 0.8649 (mtt180) cc_final: 0.8378 (mtp-110) REVERT: C 807 MET cc_start: 0.8999 (mtm) cc_final: 0.8658 (mtm) REVERT: D 594 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8460 (mtm110) REVERT: F 11 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7904 (tm) REVERT: F 65 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7335 (mtp85) REVERT: F 83 PHE cc_start: 0.7217 (m-80) cc_final: 0.6921 (m-80) REVERT: F 204 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7491 (ttm170) REVERT: F 207 GLN cc_start: 0.7206 (tt0) cc_final: 0.6969 (tm-30) REVERT: G 65 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7322 (mtm-85) REVERT: G 131 ARG cc_start: 0.6860 (tpp80) cc_final: 0.6568 (tpp80) REVERT: G 205 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6544 (t-90) REVERT: H 99 ARG cc_start: 0.7996 (mmt180) cc_final: 0.7573 (tpp80) outliers start: 31 outliers final: 13 residues processed: 193 average time/residue: 1.5608 time to fit residues: 322.0742 Evaluate side-chains 178 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.1980 chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS H 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10916 Z= 0.236 Angle : 0.509 7.196 14694 Z= 0.272 Chirality : 0.039 0.199 1628 Planarity : 0.004 0.041 1760 Dihedral : 12.246 89.871 1713 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.17 % Allowed : 15.49 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.24), residues: 1286 helix: 2.98 (0.17), residues: 920 sheet: -1.72 (1.33), residues: 12 loop : -2.09 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.004 0.001 HIS E 132 PHE 0.016 0.001 PHE G 127 TYR 0.014 0.001 TYR B 523 ARG 0.006 0.001 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.125 Fit side-chains REVERT: B 594 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: B 626 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (p) REVERT: C 594 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8339 (mtp-110) REVERT: D 594 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8436 (mtm110) REVERT: E 73 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6258 (p90) REVERT: E 122 ILE cc_start: 0.8039 (mm) cc_final: 0.7519 (tt) REVERT: E 131 ARG cc_start: 0.5884 (mmm160) cc_final: 0.5419 (mtt90) REVERT: F 11 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7870 (tm) REVERT: F 65 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7340 (mtp85) REVERT: F 73 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5753 (p90) REVERT: F 83 PHE cc_start: 0.7222 (m-80) cc_final: 0.6910 (m-80) REVERT: F 204 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7493 (ttm170) REVERT: F 207 GLN cc_start: 0.7178 (tt0) cc_final: 0.6941 (tm-30) REVERT: G 131 ARG cc_start: 0.6948 (tpp80) cc_final: 0.6679 (tpp80) REVERT: G 205 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6509 (t-90) REVERT: H 99 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7498 (tpp80) outliers start: 34 outliers final: 11 residues processed: 187 average time/residue: 1.3845 time to fit residues: 276.4125 Evaluate side-chains 178 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 205 HIS H 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10916 Z= 0.161 Angle : 0.487 7.882 14694 Z= 0.259 Chirality : 0.038 0.244 1628 Planarity : 0.004 0.038 1760 Dihedral : 11.439 87.202 1713 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.43 % Allowed : 16.51 % Favored : 81.06 % 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: 2.82 (0.24), residues: 1286 helix: 3.24 (0.17), residues: 921 sheet: -1.72 (1.36), residues: 12 loop : -2.06 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.003 0.001 HIS E 132 PHE 0.014 0.001 PHE G 127 TYR 0.013 0.001 TYR B 523 ARG 0.007 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.157 Fit side-chains REVERT: B 509 LYS cc_start: 0.7502 (tmmt) cc_final: 0.7259 (tttp) REVERT: B 594 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: B 626 VAL cc_start: 0.8835 (m) cc_final: 0.8630 (p) REVERT: C 594 ARG cc_start: 0.8636 (mtt180) cc_final: 0.8384 (mpp80) REVERT: D 594 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8461 (mtm110) REVERT: E 5 ASP cc_start: 0.2604 (OUTLIER) cc_final: 0.2372 (p0) REVERT: E 73 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6298 (p90) REVERT: E 131 ARG cc_start: 0.5902 (mmm160) cc_final: 0.5460 (mtt90) REVERT: F 11 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7859 (tm) REVERT: F 65 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7439 (mtp85) REVERT: F 73 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5713 (p90) REVERT: F 204 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7485 (ttm170) REVERT: F 207 GLN cc_start: 0.7280 (tt0) cc_final: 0.7062 (tm-30) REVERT: H 99 ARG cc_start: 0.7898 (mmt180) cc_final: 0.7473 (tpp80) outliers start: 26 outliers final: 13 residues processed: 183 average time/residue: 1.3938 time to fit residues: 272.0882 Evaluate side-chains 180 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 149 ASN G 205 HIS H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10916 Z= 0.140 Angle : 0.468 6.430 14694 Z= 0.249 Chirality : 0.037 0.192 1628 Planarity : 0.004 0.037 1760 Dihedral : 10.878 86.038 1712 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.26 % Allowed : 16.51 % Favored : 80.22 % 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: 3.06 (0.24), residues: 1286 helix: 3.39 (0.17), residues: 921 sheet: -0.17 (1.34), residues: 10 loop : -1.93 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.004 0.001 HIS E 132 PHE 0.018 0.001 PHE F 127 TYR 0.014 0.001 TYR B 523 ARG 0.007 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 1.251 Fit side-chains REVERT: A 627 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7892 (mp0) REVERT: B 509 LYS cc_start: 0.7472 (tmmt) cc_final: 0.7214 (tttp) REVERT: B 594 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8483 (mtt180) REVERT: C 594 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8396 (mpp80) REVERT: D 594 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8463 (mtm110) REVERT: E 5 ASP cc_start: 0.2879 (OUTLIER) cc_final: 0.2645 (p0) REVERT: E 73 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6215 (p90) REVERT: E 122 ILE cc_start: 0.7874 (mm) cc_final: 0.7471 (tt) REVERT: F 11 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7894 (tm) REVERT: F 65 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7404 (mtp85) REVERT: F 73 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5748 (p90) REVERT: F 83 PHE cc_start: 0.7193 (m-80) cc_final: 0.6878 (m-80) REVERT: G 131 ARG cc_start: 0.6898 (tpp80) cc_final: 0.6665 (tpp80) REVERT: H 99 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7480 (tpp80) outliers start: 35 outliers final: 12 residues processed: 187 average time/residue: 1.4028 time to fit residues: 279.7928 Evaluate side-chains 175 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 205 HIS G 160 ASN G 205 HIS H 132 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10916 Z= 0.166 Angle : 0.478 7.401 14694 Z= 0.253 Chirality : 0.037 0.185 1628 Planarity : 0.004 0.036 1760 Dihedral : 10.706 85.229 1712 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.99 % Allowed : 16.60 % Favored : 80.41 % 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: 3.07 (0.24), residues: 1286 helix: 3.36 (0.17), residues: 923 sheet: -0.06 (1.35), residues: 10 loop : -1.84 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 178 HIS 0.008 0.001 HIS E 132 PHE 0.018 0.001 PHE G 127 TYR 0.015 0.001 TYR G 128 ARG 0.007 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.155 Fit side-chains REVERT: B 509 LYS cc_start: 0.7430 (tmmt) cc_final: 0.7197 (tttp) REVERT: B 594 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8493 (mtt180) REVERT: C 594 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8412 (mpp80) REVERT: D 594 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8455 (mtm110) REVERT: E 5 ASP cc_start: 0.2899 (OUTLIER) cc_final: 0.2686 (p0) REVERT: E 73 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6284 (p90) REVERT: E 122 ILE cc_start: 0.7887 (mm) cc_final: 0.7543 (tt) REVERT: F 11 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (tm) REVERT: F 65 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7420 (mtp85) REVERT: F 73 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5684 (p90) REVERT: F 83 PHE cc_start: 0.7129 (m-80) cc_final: 0.6816 (m-80) REVERT: G 131 ARG cc_start: 0.6833 (tpp80) cc_final: 0.6597 (tpp80) REVERT: H 99 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7503 (tpp80) outliers start: 32 outliers final: 15 residues processed: 185 average time/residue: 1.3748 time to fit residues: 271.5895 Evaluate side-chains 175 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 160 ASN G 205 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10916 Z= 0.148 Angle : 0.498 11.176 14694 Z= 0.261 Chirality : 0.037 0.217 1628 Planarity : 0.004 0.036 1760 Dihedral : 10.532 85.806 1712 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.52 % Allowed : 17.35 % Favored : 80.13 % 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: 3.14 (0.24), residues: 1286 helix: 3.42 (0.17), residues: 921 sheet: 0.11 (1.40), residues: 10 loop : -1.82 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 178 HIS 0.004 0.001 HIS F 132 PHE 0.009 0.001 PHE G 73 TYR 0.015 0.001 TYR B 523 ARG 0.007 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.285 Fit side-chains REVERT: A 627 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8091 (tp30) REVERT: B 594 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8496 (mtt180) REVERT: C 594 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8409 (mpp80) REVERT: D 594 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8449 (mtm110) REVERT: E 5 ASP cc_start: 0.2857 (OUTLIER) cc_final: 0.2642 (p0) REVERT: E 73 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6304 (p90) REVERT: E 122 ILE cc_start: 0.7865 (mm) cc_final: 0.7508 (tt) REVERT: F 11 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7890 (tm) REVERT: F 65 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7240 (mtp85) REVERT: F 66 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8235 (t) REVERT: F 73 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5595 (p90) REVERT: F 83 PHE cc_start: 0.7100 (m-80) cc_final: 0.6793 (m-80) REVERT: G 131 ARG cc_start: 0.6911 (tpp80) cc_final: 0.6685 (tpp80) REVERT: H 99 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7473 (ttp80) outliers start: 27 outliers final: 12 residues processed: 184 average time/residue: 1.3924 time to fit residues: 274.2747 Evaluate side-chains 174 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 160 ASN G 205 HIS H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10916 Z= 0.146 Angle : 0.487 9.191 14694 Z= 0.258 Chirality : 0.037 0.185 1628 Planarity : 0.004 0.036 1760 Dihedral : 10.217 86.962 1712 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.80 % Allowed : 17.26 % Favored : 79.94 % 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: 3.16 (0.24), residues: 1286 helix: 3.43 (0.17), residues: 922 sheet: 0.07 (1.58), residues: 10 loop : -1.79 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 551 HIS 0.004 0.001 HIS F 132 PHE 0.021 0.001 PHE G 127 TYR 0.016 0.001 TYR G 128 ARG 0.007 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.152 Fit side-chains REVERT: A 627 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7946 (mp0) REVERT: B 594 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8479 (mtt180) REVERT: C 594 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8361 (mpp80) REVERT: D 594 ARG cc_start: 0.8873 (mtt180) cc_final: 0.8457 (mtm110) REVERT: E 73 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6343 (p90) REVERT: E 122 ILE cc_start: 0.7865 (mm) cc_final: 0.7523 (tt) REVERT: F 65 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7224 (mtp85) REVERT: F 66 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8091 (t) REVERT: F 73 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.5626 (p90) REVERT: F 83 PHE cc_start: 0.7074 (m-80) cc_final: 0.6768 (m-80) REVERT: H 99 ARG cc_start: 0.7895 (mmt180) cc_final: 0.7461 (ttp80) outliers start: 30 outliers final: 13 residues processed: 184 average time/residue: 1.3404 time to fit residues: 263.7117 Evaluate side-chains 174 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 0.0670 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 205 HIS F 149 ASN G 160 ASN G 205 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10916 Z= 0.165 Angle : 0.497 9.780 14694 Z= 0.262 Chirality : 0.037 0.183 1628 Planarity : 0.004 0.035 1760 Dihedral : 10.101 82.769 1712 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.96 % Allowed : 18.28 % Favored : 79.76 % 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: 3.10 (0.24), residues: 1286 helix: 3.39 (0.17), residues: 923 sheet: 0.02 (1.61), residues: 10 loop : -1.85 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 551 HIS 0.008 0.001 HIS E 132 PHE 0.009 0.001 PHE B 584 TYR 0.016 0.001 TYR B 523 ARG 0.007 0.001 ARG D 586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.221 Fit side-chains REVERT: A 627 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8100 (tp30) REVERT: B 511 LYS cc_start: 0.8449 (tptm) cc_final: 0.8168 (pptt) REVERT: B 594 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8476 (mtt180) REVERT: C 594 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8373 (mpp80) REVERT: D 551 TRP cc_start: 0.5732 (m100) cc_final: 0.5396 (m100) REVERT: D 594 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8460 (mtm110) REVERT: E 73 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6289 (p90) REVERT: E 122 ILE cc_start: 0.7914 (mm) cc_final: 0.7573 (tt) REVERT: F 65 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7266 (mtp85) REVERT: F 66 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7780 (t) REVERT: F 73 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5633 (p90) REVERT: F 83 PHE cc_start: 0.7102 (m-80) cc_final: 0.6763 (m-80) REVERT: G 131 ARG cc_start: 0.6796 (tpp80) cc_final: 0.6529 (tpp80) REVERT: H 99 ARG cc_start: 0.7894 (mmt180) cc_final: 0.7465 (ttp80) outliers start: 21 outliers final: 14 residues processed: 176 average time/residue: 1.3848 time to fit residues: 260.1272 Evaluate side-chains 173 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 205 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.090224 restraints weight = 48401.949| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 5.56 r_work: 0.2569 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 10916 Z= 0.253 Angle : 0.800 59.197 14694 Z= 0.485 Chirality : 0.040 0.655 1628 Planarity : 0.004 0.056 1760 Dihedral : 10.142 82.735 1712 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 2.05 % Allowed : 18.47 % Favored : 79.48 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 3.08 (0.24), residues: 1286 helix: 3.38 (0.17), residues: 923 sheet: 0.01 (1.61), residues: 10 loop : -1.87 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 551 HIS 0.010 0.001 HIS F 132 PHE 0.009 0.001 PHE B 584 TYR 0.016 0.001 TYR B 523 ARG 0.007 0.000 ARG D 586 =============================================================================== Job complete usr+sys time: 4534.66 seconds wall clock time: 82 minutes 48.07 seconds (4968.07 seconds total)