Starting phenix.real_space_refine on Thu Feb 15 19:18:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/02_2024/8i0z_35114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/02_2024/8i0z_35114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/02_2024/8i0z_35114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/02_2024/8i0z_35114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/02_2024/8i0z_35114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0z_35114/02_2024/8i0z_35114_updated.pdb" } resolution = 4.33 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= 0.015 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 15 5.49 5 S 24 5.16 5 C 8342 2.51 5 N 2234 2.21 5 O 2548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 146": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 18": "OD1" <-> "OD2" 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: 13163 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2620 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2620 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2595 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 910 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Chain: "N" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "V" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 6.93, per 1000 atoms: 0.53 Number of scatterers: 13163 At special positions: 0 Unit cell: (149.844, 151.093, 89.9064, 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 24 16.00 P 15 15.00 O 2548 8.00 N 2234 7.00 C 8342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.05 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.04 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " 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: 4.88 Conformation dependent library (CDL) restraints added in 2.4 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 30 sheets defined 4.2% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'M' and resid 32 through 34 No H-bonds generated for 'chain 'M' and resid 32 through 34' Processing helix chain 'M' and resid 65 through 67 No H-bonds generated for 'chain 'M' and resid 65 through 67' Processing sheet with id= A, first strand: chain 'A' and resid 10 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.766A pdb=" N ARG A 170 " --> pdb=" O PHE A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.500A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 148 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 190 Processing sheet with id= F, first strand: chain 'A' and resid 336 through 342 removed outlier: 4.309A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 10 through 13 Processing sheet with id= H, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.798A pdb=" N ARG B 170 " --> pdb=" O PHE B 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.059A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 60 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE B 82 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= K, first strand: chain 'B' and resid 184 through 190 Processing sheet with id= L, first strand: chain 'B' and resid 336 through 342 removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 10 through 13 Processing sheet with id= N, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.722A pdb=" N ARG C 170 " --> pdb=" O PHE C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.006A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 56 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN C 86 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU C 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 60 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 82 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= Q, first strand: chain 'C' and resid 184 through 187 Processing sheet with id= R, first strand: chain 'C' and resid 336 through 342 removed outlier: 3.528A pdb=" N PHE C 342 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 242 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLN C 249 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.682A pdb=" N GLN D 6 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.854A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D 62 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= V, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= W, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.577A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.848A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 53 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'L' and resid 86 through 91 removed outlier: 4.403A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 39 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 23 through 26 Processing sheet with id= AB, first strand: chain 'M' and resid 117 through 119 removed outlier: 3.990A pdb=" N ALA M 52 " --> pdb=" O TRP M 39 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG M 41 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TRP M 50 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR M 62 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR M 60 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AD, first strand: chain 'N' and resid 87 through 91 removed outlier: 3.544A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1044 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: 3.67 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4237 1.34 - 1.47: 3295 1.47 - 1.59: 5854 1.59 - 1.71: 40 1.71 - 1.83: 33 Bond restraints: 13459 Sorted by residual: bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 13454 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.10: 463 107.10 - 113.84: 7559 113.84 - 120.59: 4787 120.59 - 127.33: 5388 127.33 - 134.08: 149 Bond angle restraints: 18346 Sorted by residual: angle pdb=" N GLY D 12 " pdb=" CA GLY D 12 " pdb=" C GLY D 12 " ideal model delta sigma weight residual 111.42 120.68 -9.26 1.51e+00 4.39e-01 3.76e+01 angle pdb=" C PHE H 105 " pdb=" N TRP H 106 " pdb=" CA TRP H 106 " ideal model delta sigma weight residual 121.70 129.23 -7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" N GLU A 314 " pdb=" CA GLU A 314 " pdb=" CB GLU A 314 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" C PHE D 105 " pdb=" N TRP D 106 " pdb=" CA TRP D 106 " ideal model delta sigma weight residual 121.70 128.77 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C PHE M 105 " pdb=" N TRP M 106 " pdb=" CA TRP M 106 " ideal model delta sigma weight residual 121.70 128.75 -7.05 1.80e+00 3.09e-01 1.53e+01 ... (remaining 18341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7454 17.96 - 35.93: 463 35.93 - 53.89: 68 53.89 - 71.85: 15 71.85 - 89.82: 10 Dihedral angle restraints: 8010 sinusoidal: 2988 harmonic: 5022 Sorted by residual: dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 40.30 52.70 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CA MET H 86 " pdb=" C MET H 86 " pdb=" N ASN H 87 " pdb=" CA ASN H 87 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA MET D 86 " pdb=" C MET D 86 " pdb=" N ASN D 87 " pdb=" CA ASN D 87 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1371 0.038 - 0.076: 461 0.076 - 0.115: 190 0.115 - 0.153: 65 0.153 - 0.191: 9 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CG LEU M 7 " pdb=" CB LEU M 7 " pdb=" CD1 LEU M 7 " pdb=" CD2 LEU M 7 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CB ILE L 107 " pdb=" CA ILE L 107 " pdb=" CG1 ILE L 107 " pdb=" CG2 ILE L 107 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB ILE E 76 " pdb=" CA ILE E 76 " pdb=" CG1 ILE E 76 " pdb=" CG2 ILE E 76 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2093 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 107 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ILE N 107 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE N 107 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS N 108 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 341 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 124 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO C 125 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.025 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 163 2.63 - 3.20: 12593 3.20 - 3.77: 19261 3.77 - 4.33: 25692 4.33 - 4.90: 42458 Nonbonded interactions: 100167 Sorted by model distance: nonbonded pdb=" NE2 GLN E 39 " pdb=" O LYS E 40 " model vdw 2.066 2.520 nonbonded pdb=" NE2 GLN L 39 " pdb=" O LYS L 40 " model vdw 2.095 2.520 nonbonded pdb=" NE2 GLN N 39 " pdb=" O LYS N 40 " model vdw 2.109 2.520 nonbonded pdb=" OD1 ASP N 18 " pdb=" N ARG N 19 " model vdw 2.149 2.520 nonbonded pdb=" OD1 ASP E 18 " pdb=" N ARG E 19 " model vdw 2.254 2.520 ... (remaining 100162 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 8 through 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB )) or resid 190 through 229 or (resid 23 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 231 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 through 314 or (resid 315 through 316 and (name N or name CA or name C o \ r name O or name CB )) or resid 317 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 338 or (resid 339 an \ d (name N or name CA or name C or name O or name CB )) or resid 340 through 350) \ ) selection = (chain 'B' and (resid 8 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 and (name N o \ r name CA or name C or name O or name CB )) or resid 159 through 188 or (resid 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 229 or (resid 230 and (name N or name CA or name C or name O or \ name CB )) or resid 231 through 315 or (resid 316 and (name N or name CA or nam \ e C or name O or name CB )) or resid 317 through 324 or (resid 325 and (name N o \ r name CA or name C or name O or name CB )) or resid 326 through 338 or (resid 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 350)) selection = (chain 'C' and (resid 8 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 350)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 5 through 122) selection = (chain 'M' and (resid 5 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 122)) } ncs_group { reference = (chain 'E' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 107)) selection = (chain 'L' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 107)) selection = (chain 'N' and (resid 2 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 through 107)) } ncs_group { reference = (chain 'G' and resid 334 through 342) selection = (chain 'U' and resid 334 through 342) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 10.530 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.860 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.007 0.107 13459 Z= 0.458 Angle : 0.914 11.110 18346 Z= 0.472 Chirality : 0.049 0.191 2096 Planarity : 0.006 0.059 2340 Dihedral : 12.708 89.817 4764 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.29 % Allowed : 0.58 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.50 (0.20), residues: 1672 helix: -2.36 (0.59), residues: 42 sheet: -0.64 (0.20), residues: 658 loop : -1.16 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS C 114 PHE 0.020 0.002 PHE L 99 TYR 0.028 0.002 TYR M 33 ARG 0.007 0.001 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: B 295 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7744 (ptpp) REVERT: E 36 TRP cc_start: 0.7569 (m100) cc_final: 0.7248 (m100) REVERT: E 107 ILE cc_start: 0.6561 (mp) cc_final: 0.6308 (pt) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.2208 time to fit residues: 34.0253 Evaluate side-chains 58 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 79 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 chunk 151 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN C 211 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13459 Z= 0.178 Angle : 0.650 6.834 18346 Z= 0.333 Chirality : 0.047 0.183 2096 Planarity : 0.004 0.041 2340 Dihedral : 6.454 43.390 1898 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.08 (0.20), residues: 1672 helix: -0.08 (0.80), residues: 36 sheet: -0.45 (0.18), residues: 762 loop : -0.92 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS B 346 PHE 0.018 0.001 PHE B 145 TYR 0.024 0.001 TYR M 33 ARG 0.004 0.001 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: D 68 LYS cc_start: 0.9175 (tppt) cc_final: 0.8943 (tppt) REVERT: H 103 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8277 (ttm-80) REVERT: M 31 ASN cc_start: 0.8851 (t0) cc_final: 0.8636 (t0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2017 time to fit residues: 26.6758 Evaluate side-chains 52 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 135 optimal weight: 0.0050 chunk 150 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13459 Z= 0.293 Angle : 0.689 9.419 18346 Z= 0.355 Chirality : 0.047 0.285 2096 Planarity : 0.004 0.046 2340 Dihedral : 6.140 37.732 1898 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.10 (0.20), residues: 1672 helix: 0.64 (0.90), residues: 36 sheet: -0.34 (0.19), residues: 772 loop : -1.10 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 106 HIS 0.005 0.001 HIS C 346 PHE 0.014 0.002 PHE B 145 TYR 0.015 0.002 TYR A 209 ARG 0.003 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.578 Fit side-chains REVERT: E 36 TRP cc_start: 0.7877 (m100) cc_final: 0.7116 (m100) REVERT: E 74 LEU cc_start: 0.9276 (tp) cc_final: 0.9040 (tp) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.1842 time to fit residues: 23.9050 Evaluate side-chains 52 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 13459 Z= 0.335 Angle : 0.682 10.601 18346 Z= 0.352 Chirality : 0.046 0.354 2096 Planarity : 0.004 0.044 2340 Dihedral : 6.043 36.293 1898 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.19 (0.20), residues: 1672 helix: 0.70 (0.94), residues: 36 sheet: -0.32 (0.19), residues: 757 loop : -1.25 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 39 HIS 0.004 0.001 HIS A 114 PHE 0.021 0.002 PHE E 99 TYR 0.016 0.002 TYR B 209 ARG 0.006 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.862 Fit side-chains REVERT: E 36 TRP cc_start: 0.7950 (m100) cc_final: 0.7249 (m100) REVERT: E 74 LEU cc_start: 0.9225 (tp) cc_final: 0.8934 (tp) REVERT: M 86 MET cc_start: 0.8345 (ppp) cc_final: 0.8090 (ppp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1952 time to fit residues: 23.9936 Evaluate side-chains 51 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13459 Z= 0.215 Angle : 0.605 8.774 18346 Z= 0.307 Chirality : 0.044 0.278 2096 Planarity : 0.004 0.037 2340 Dihedral : 5.583 34.532 1898 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.07 (0.20), residues: 1672 helix: 0.97 (0.90), residues: 36 sheet: -0.21 (0.19), residues: 765 loop : -1.22 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS A 296 PHE 0.021 0.001 PHE E 99 TYR 0.016 0.001 TYR M 33 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.532 Fit side-chains REVERT: E 36 TRP cc_start: 0.7824 (m100) cc_final: 0.7288 (m100) REVERT: E 74 LEU cc_start: 0.9147 (tp) cc_final: 0.8778 (tp) REVERT: E 94 TYR cc_start: 0.9215 (m-80) cc_final: 0.8978 (m-10) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1794 time to fit residues: 24.2359 Evaluate side-chains 51 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 161 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13459 Z= 0.278 Angle : 0.638 9.753 18346 Z= 0.326 Chirality : 0.046 0.365 2096 Planarity : 0.004 0.038 2340 Dihedral : 5.683 34.204 1898 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.09 (0.20), residues: 1672 helix: 0.80 (0.91), residues: 36 sheet: -0.10 (0.20), residues: 750 loop : -1.34 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 39 HIS 0.004 0.001 HIS A 114 PHE 0.019 0.002 PHE E 99 TYR 0.012 0.001 TYR M 33 ARG 0.007 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.520 Fit side-chains REVERT: E 36 TRP cc_start: 0.7985 (m100) cc_final: 0.7334 (m100) REVERT: E 74 LEU cc_start: 0.9166 (tp) cc_final: 0.8787 (tp) REVERT: E 94 TYR cc_start: 0.9198 (m-80) cc_final: 0.8965 (m-10) REVERT: M 86 MET cc_start: 0.7767 (pmm) cc_final: 0.7531 (pmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1937 time to fit residues: 24.0406 Evaluate side-chains 51 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 160 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13459 Z= 0.171 Angle : 0.575 8.638 18346 Z= 0.288 Chirality : 0.044 0.201 2096 Planarity : 0.004 0.033 2340 Dihedral : 5.274 32.673 1898 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1672 helix: 0.87 (0.82), residues: 36 sheet: 0.06 (0.19), residues: 755 loop : -1.32 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.003 0.001 HIS H 38 PHE 0.018 0.001 PHE E 99 TYR 0.010 0.001 TYR L 50 ARG 0.003 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.498 Fit side-chains REVERT: D 99 CYS cc_start: 0.2994 (p) cc_final: 0.2761 (p) REVERT: E 36 TRP cc_start: 0.7807 (m100) cc_final: 0.7377 (m100) REVERT: E 74 LEU cc_start: 0.9092 (tp) cc_final: 0.8712 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1785 time to fit residues: 25.6483 Evaluate side-chains 53 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13459 Z= 0.238 Angle : 0.606 9.786 18346 Z= 0.307 Chirality : 0.044 0.289 2096 Planarity : 0.004 0.038 2340 Dihedral : 5.386 32.678 1898 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1672 helix: 0.90 (0.86), residues: 36 sheet: 0.01 (0.19), residues: 779 loop : -1.32 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 39 HIS 0.004 0.001 HIS C 114 PHE 0.020 0.002 PHE L 99 TYR 0.010 0.001 TYR L 37 ARG 0.002 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.592 Fit side-chains REVERT: D 68 LYS cc_start: 0.8914 (tppt) cc_final: 0.8628 (tppt) REVERT: E 36 TRP cc_start: 0.7867 (m100) cc_final: 0.7279 (m100) REVERT: E 74 LEU cc_start: 0.9128 (tp) cc_final: 0.8733 (tp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1728 time to fit residues: 24.1972 Evaluate side-chains 55 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 13459 Z= 0.328 Angle : 0.672 9.524 18346 Z= 0.345 Chirality : 0.046 0.374 2096 Planarity : 0.004 0.043 2340 Dihedral : 5.756 33.849 1898 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.13 (0.21), residues: 1672 helix: 0.84 (0.94), residues: 34 sheet: -0.04 (0.19), residues: 770 loop : -1.49 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 106 HIS 0.005 0.001 HIS C 114 PHE 0.031 0.002 PHE L 99 TYR 0.014 0.002 TYR L 37 ARG 0.005 0.000 ARG M 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: D 68 LYS cc_start: 0.8937 (tppt) cc_final: 0.8628 (tppt) REVERT: N 38 GLN cc_start: 0.8721 (pp30) cc_final: 0.8424 (pp30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1767 time to fit residues: 25.4214 Evaluate side-chains 56 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 0.0040 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13459 Z= 0.230 Angle : 0.609 8.555 18346 Z= 0.308 Chirality : 0.045 0.304 2096 Planarity : 0.004 0.035 2340 Dihedral : 5.477 34.351 1898 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % 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: -1.05 (0.21), residues: 1672 helix: 0.86 (0.88), residues: 34 sheet: 0.02 (0.20), residues: 775 loop : -1.46 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 39 HIS 0.004 0.001 HIS C 114 PHE 0.025 0.002 PHE L 99 TYR 0.012 0.001 TYR L 37 ARG 0.003 0.000 ARG M 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.485 Fit side-chains REVERT: D 68 LYS cc_start: 0.8917 (tppt) cc_final: 0.8594 (tppt) REVERT: E 36 TRP cc_start: 0.7811 (m100) cc_final: 0.7270 (m100) REVERT: H 68 LYS cc_start: 0.8942 (tppt) cc_final: 0.8541 (tppt) REVERT: N 38 GLN cc_start: 0.8778 (pp30) cc_final: 0.8481 (tm-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1828 time to fit residues: 25.7298 Evaluate side-chains 54 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 0.0010 chunk 7 optimal weight: 7.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.080731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.069958 restraints weight = 73585.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072473 restraints weight = 81629.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072881 restraints weight = 35100.838| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13459 Z= 0.222 Angle : 0.607 8.500 18346 Z= 0.305 Chirality : 0.045 0.302 2096 Planarity : 0.004 0.037 2340 Dihedral : 5.373 35.277 1898 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1672 helix: 0.93 (0.89), residues: 34 sheet: 0.11 (0.20), residues: 767 loop : -1.41 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 39 HIS 0.004 0.001 HIS C 114 PHE 0.024 0.002 PHE L 99 TYR 0.011 0.001 TYR L 37 ARG 0.003 0.000 ARG M 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.77 seconds wall clock time: 40 minutes 32.43 seconds (2432.43 seconds total)