Starting phenix.real_space_refine on Thu Feb 15 19:32:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/02_2024/8i10_35115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/02_2024/8i10_35115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/02_2024/8i10_35115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/02_2024/8i10_35115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/02_2024/8i10_35115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/02_2024/8i10_35115_updated.pdb" } resolution = 3.96 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= 0.001 sd= 0.021 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 8375 2.51 5 N 2264 2.21 5 O 2518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 13196 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2641 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2632 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2603 Classifications: {'peptide': 343} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 908 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 786 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 797 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.04, per 1000 atoms: 0.53 Number of scatterers: 13196 At special positions: 0 Unit cell: (149.274, 143.443, 90.9636, 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 2518 8.00 N 2264 7.00 C 8375 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=2.04 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=2.04 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: 5.18 Conformation dependent library (CDL) restraints added in 2.3 seconds 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 34 sheets defined 2.6% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 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 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 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' 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: 6.633A 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: 3.536A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.871A 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: 3.515A pdb=" N PHE A 342 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (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: 6.631A 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 167 removed outlier: 3.505A pdb=" N ARG B 63 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (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: 3.565A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.811A pdb=" N PHE B 81 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 62 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 79 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 10 through 13 Processing sheet with id= O, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.392A pdb=" N ARG C 170 " --> pdb=" O PHE C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.836A pdb=" N ILE C 169 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 63 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 56 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN C 86 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASN C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 60 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE C 82 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= R, first strand: chain 'C' and resid 184 through 190 Processing sheet with id= S, first strand: chain 'C' and resid 336 through 342 removed outlier: 3.523A pdb=" N PHE C 342 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 242 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN C 249 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 6 through 10 Processing sheet with id= U, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.255A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 100 through 102 removed outlier: 4.033A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= X, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.091A pdb=" N LYS E 104 " --> pdb=" O LEU E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.561A pdb=" N ILE E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= AA, first strand: chain 'H' and resid 117 through 119 removed outlier: 6.406A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= AC, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.124A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ALA L 14 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU L 106 " --> pdb=" O ALA L 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'L' and resid 86 through 91 removed outlier: 6.235A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 6 through 10 Processing sheet with id= AF, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.414A pdb=" N ARG M 41 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP M 50 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR M 60 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AH, first strand: chain 'N' and resid 86 through 91 removed outlier: 6.275A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1152 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: 3.60 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4025 1.33 - 1.46: 3142 1.46 - 1.58: 6265 1.58 - 1.71: 39 1.71 - 1.83: 33 Bond restraints: 13504 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.597 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" OG1 TPO U 360 " pdb=" P TPO U 360 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 ... (remaining 13499 not shown) Histogram of bond angle deviations from ideal: 96.63 - 104.11: 262 104.11 - 111.59: 6023 111.59 - 119.08: 4733 119.08 - 126.56: 7188 126.56 - 134.04: 197 Bond angle restraints: 18403 Sorted by residual: angle pdb=" C SEP V 363 " pdb=" N SEP V 364 " pdb=" CA SEP V 364 " ideal model delta sigma weight residual 121.70 111.72 9.98 1.80e+00 3.09e-01 3.07e+01 angle pdb=" N SER B 75 " pdb=" CA SER B 75 " pdb=" C SER B 75 " ideal model delta sigma weight residual 110.80 120.21 -9.41 2.13e+00 2.20e-01 1.95e+01 angle pdb=" CA GLN C 182 " pdb=" CB GLN C 182 " pdb=" CG GLN C 182 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA LYS A 108 " pdb=" CB LYS A 108 " pdb=" CG LYS A 108 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA LEU V 365 " pdb=" C LEU V 365 " pdb=" N ALA V 366 " ideal model delta sigma weight residual 116.20 124.15 -7.95 2.00e+00 2.50e-01 1.58e+01 ... (remaining 18398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7353 17.93 - 35.86: 585 35.86 - 53.79: 85 53.79 - 71.72: 15 71.72 - 89.65: 19 Dihedral angle restraints: 8057 sinusoidal: 3026 harmonic: 5031 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA THR N 98 " pdb=" C THR N 98 " pdb=" N PHE N 99 " pdb=" CA PHE N 99 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA LEU C 74 " pdb=" C LEU C 74 " pdb=" N SER C 75 " pdb=" CA SER C 75 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 8054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1718 0.070 - 0.141: 332 0.141 - 0.211: 30 0.211 - 0.281: 7 0.281 - 0.351: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" CG LEU B 49 " pdb=" CB LEU B 49 " pdb=" CD1 LEU B 49 " pdb=" CD2 LEU B 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CG LEU M 21 " pdb=" CB LEU M 21 " pdb=" CD1 LEU M 21 " pdb=" CD2 LEU M 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2086 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 71 " 0.036 2.00e-02 2.50e+03 3.91e-02 2.67e+01 pdb=" CG PHE H 71 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE H 71 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 71 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE H 71 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE H 71 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 71 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 71 " 0.028 2.00e-02 2.50e+03 3.13e-02 1.71e+01 pdb=" CG PHE D 71 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D 71 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 71 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE D 71 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE D 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 71 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 209 " 0.015 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR A 209 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 209 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 209 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 209 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 209 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 209 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 209 " -0.003 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 729 2.72 - 3.26: 13277 3.26 - 3.81: 19646 3.81 - 4.35: 23405 4.35 - 4.90: 42287 Nonbonded interactions: 99344 Sorted by model distance: nonbonded pdb=" O SER L 29 " pdb=" OG SER L 29 " model vdw 2.172 2.440 nonbonded pdb=" O SER M 34 " pdb=" OG SER M 34 " model vdw 2.211 2.440 nonbonded pdb=" O ASN D 31 " pdb=" OG SER D 35 " model vdw 2.222 2.440 nonbonded pdb=" NZ LYS C 108 " pdb=" OG SEP V 363 " model vdw 2.266 2.520 nonbonded pdb=" O SER E 32 " pdb=" OG SER E 32 " model vdw 2.268 2.440 ... (remaining 99339 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 7 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 49 or (resid 50 and \ (name N or name CA or name C or name O )) or (resid 51 and (name N or name CA or \ name C or name O or name CB )) or resid 52 through 73 or (resid 74 through 76 a \ nd (name N or name CA or name C or name O or name CB )) or resid 77 through 84 o \ r (resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 \ through 102 or (resid 103 and (name N or name CA or name C or name O or name CB \ )) or resid 104 through 110 or (resid 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 185 or (resid 186 and ( \ name N or name CA or name C or name O or name CB )) or resid 187 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 283 or (resid 284 and (name N or name CA or name C or name O or name CB \ )) or resid 285 through 295 or (resid 296 and (name N or name CA or name C or n \ ame O or name CB )) or resid 297 through 311 or (resid 312 and (name N or name C \ A or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and ( \ name N or name CA or name C or name O or name CB )) or resid 316 through 350)) selection = (chain 'B' and (resid 7 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or (resid 51 and (name N or name CA or name C or name \ O or name CB )) or resid 52 through 75 or (resid 76 and (name N or name CA or n \ ame C or name O or name CB )) or resid 77 through 84 or (resid 85 and (name N or \ name CA or name C or name O or name CB )) or resid 86 through 102 or (resid 103 \ and (name N or name CA or name C or name O or name CB )) or resid 104 through 1 \ 10 or (resid 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 113 or (resid 114 and (name N or name CA or name C or name O or n \ ame CB )) or resid 115 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 156 or (resid 157 through 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 176 o \ r (resid 177 through 178 and (name N or name CA or name C or name O or name CB ) \ ) or resid 179 through 229 or (resid 230 and (name N or name CA or name C or nam \ e O or name CB )) or resid 231 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 through 295 or (resid 296 and (na \ me N or name CA or name C or name O or name CB )) or resid 297 through 350)) selection = (chain 'C' and (resid 7 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 92 or (resid 93 and (n \ ame N or name CA or name C or name O or name CB )) or resid 94 through 176 or (r \ esid 177 through 178 and (name N or name CA or name C or name O or name CB )) or \ resid 179 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 229 or (resid 230 and (name N \ or name CA or name C or name O or name CB )) or resid 231 through 311 or (resid \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 350)) } ncs_group { reference = (chain 'D' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 13 or (resid 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 45 or (resid 46 and (name \ N or name CA or name C or name O or name CB )) or resid 47 through 121)) selection = (chain 'H' and (resid 5 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 45 or (resid 46 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 121)) selection = (chain 'M' and resid 5 through 121) } ncs_group { reference = (chain 'E' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 106)) selection = (chain 'L' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 106)) selection = (chain 'N' and resid 2 through 106) } ncs_group { reference = chain 'G' selection = chain 'U' 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: 3.400 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: 10.560 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.980 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.006 0.120 13504 Z= 0.393 Angle : 0.951 9.977 18403 Z= 0.486 Chirality : 0.055 0.351 2089 Planarity : 0.007 0.063 2344 Dihedral : 13.994 89.646 4805 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.58 % Allowed : 16.20 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 1681 helix: -0.54 (0.80), residues: 36 sheet: -0.41 (0.18), residues: 769 loop : -0.92 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 36 HIS 0.011 0.002 HIS B 112 PHE 0.089 0.003 PHE H 71 TYR 0.061 0.003 TYR A 209 ARG 0.009 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: H 80 ASN cc_start: 0.7625 (t0) cc_final: 0.7362 (t0) outliers start: 8 outliers final: 7 residues processed: 179 average time/residue: 0.2283 time to fit residues: 61.0069 Evaluate side-chains 161 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0000 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 160 HIS A 199 HIS B 86 GLN B 112 HIS B 182 GLN H 85 GLN M 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13504 Z= 0.181 Angle : 0.662 9.711 18403 Z= 0.336 Chirality : 0.046 0.166 2089 Planarity : 0.005 0.055 2344 Dihedral : 6.932 88.664 1921 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.11 % Allowed : 15.33 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.68 (0.20), residues: 1681 helix: 0.82 (0.85), residues: 36 sheet: -0.01 (0.19), residues: 769 loop : -0.86 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 50 HIS 0.005 0.001 HIS A 346 PHE 0.028 0.002 PHE C 278 TYR 0.016 0.001 TYR N 92 ARG 0.009 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8402 (p0) cc_final: 0.8109 (p0) REVERT: C 39 ASP cc_start: 0.8531 (p0) cc_final: 0.8322 (p0) REVERT: C 266 SER cc_start: 0.7923 (m) cc_final: 0.7659 (p) REVERT: D 9 GLU cc_start: 0.7094 (pm20) cc_final: 0.6734 (pt0) REVERT: M 21 LEU cc_start: 0.7747 (tp) cc_final: 0.7255 (tt) REVERT: N 6 THR cc_start: 0.8613 (t) cc_final: 0.8398 (p) outliers start: 43 outliers final: 27 residues processed: 213 average time/residue: 0.2127 time to fit residues: 68.5415 Evaluate side-chains 183 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- 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** C 160 HIS C 249 GLN D 42 GLN H 85 GLN H 104 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13504 Z= 0.300 Angle : 0.664 9.645 18403 Z= 0.340 Chirality : 0.046 0.163 2089 Planarity : 0.005 0.055 2344 Dihedral : 6.755 89.420 1915 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.19 % Allowed : 17.14 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.66 (0.21), residues: 1681 helix: 1.55 (0.88), residues: 36 sheet: -0.04 (0.19), residues: 773 loop : -0.85 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 50 HIS 0.003 0.001 HIS A 346 PHE 0.027 0.002 PHE B 88 TYR 0.020 0.002 TYR N 50 ARG 0.006 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 164 time to evaluate : 1.683 Fit side-chains REVERT: A 39 ASP cc_start: 0.8438 (p0) cc_final: 0.8103 (p0) REVERT: C 39 ASP cc_start: 0.8601 (p0) cc_final: 0.8300 (p0) REVERT: D 9 GLU cc_start: 0.7154 (pm20) cc_final: 0.6938 (pt0) REVERT: D 80 ASN cc_start: 0.7572 (t0) cc_final: 0.7238 (t0) REVERT: H 9 GLU cc_start: 0.6223 (mt-10) cc_final: 0.5921 (tt0) REVERT: H 42 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: L 5 MET cc_start: 0.8428 (tpp) cc_final: 0.7964 (tpp) REVERT: M 21 LEU cc_start: 0.7846 (tp) cc_final: 0.7391 (tt) REVERT: N 6 THR cc_start: 0.8814 (t) cc_final: 0.8553 (p) REVERT: N 28 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7529 (tm-30) outliers start: 58 outliers final: 44 residues processed: 199 average time/residue: 0.2239 time to fit residues: 68.4358 Evaluate side-chains 191 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 101 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 159 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** C 160 HIS H 85 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13504 Z= 0.187 Angle : 0.594 9.070 18403 Z= 0.299 Chirality : 0.044 0.161 2089 Planarity : 0.005 0.052 2344 Dihedral : 6.302 88.804 1915 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.12 % Allowed : 18.58 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.53 (0.21), residues: 1681 helix: 1.81 (0.88), residues: 36 sheet: 0.02 (0.18), residues: 785 loop : -0.74 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 39 HIS 0.003 0.001 HIS M 38 PHE 0.026 0.002 PHE B 88 TYR 0.020 0.001 TYR N 50 ARG 0.007 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 167 time to evaluate : 1.559 Fit side-chains REVERT: A 39 ASP cc_start: 0.8441 (p0) cc_final: 0.8021 (p0) REVERT: A 344 LEU cc_start: 0.8210 (tp) cc_final: 0.7876 (tp) REVERT: B 296 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7427 (m-70) REVERT: C 39 ASP cc_start: 0.8635 (p0) cc_final: 0.8304 (p0) REVERT: E 64 SER cc_start: 0.8133 (p) cc_final: 0.7451 (m) REVERT: H 8 VAL cc_start: 0.8945 (t) cc_final: 0.8700 (m) REVERT: H 9 GLU cc_start: 0.6170 (mt-10) cc_final: 0.5852 (mt-10) REVERT: L 5 MET cc_start: 0.8204 (tpp) cc_final: 0.7614 (tpp) REVERT: M 21 LEU cc_start: 0.7788 (tp) cc_final: 0.7384 (tt) REVERT: N 6 THR cc_start: 0.8777 (t) cc_final: 0.8493 (p) REVERT: N 28 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7498 (tm-30) outliers start: 57 outliers final: 44 residues processed: 204 average time/residue: 0.2090 time to fit residues: 65.8801 Evaluate side-chains 193 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13504 Z= 0.470 Angle : 0.721 9.897 18403 Z= 0.373 Chirality : 0.048 0.176 2089 Planarity : 0.005 0.059 2344 Dihedral : 6.708 85.510 1913 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 6.22 % Allowed : 18.44 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.82 (0.20), residues: 1681 helix: 1.95 (0.90), residues: 36 sheet: -0.05 (0.19), residues: 745 loop : -1.06 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP M 39 HIS 0.004 0.001 HIS D 38 PHE 0.036 0.002 PHE C 278 TYR 0.029 0.002 TYR N 92 ARG 0.005 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 147 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8458 (p0) cc_final: 0.8118 (p0) REVERT: B 296 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7824 (m-70) REVERT: C 39 ASP cc_start: 0.8522 (p0) cc_final: 0.8243 (p0) REVERT: C 273 TYR cc_start: 0.7717 (m-10) cc_final: 0.7416 (m-10) REVERT: E 91 GLN cc_start: 0.8357 (pp30) cc_final: 0.8053 (pp30) REVERT: H 8 VAL cc_start: 0.8967 (t) cc_final: 0.8729 (m) REVERT: H 9 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6137 (mt-10) REVERT: H 42 GLN cc_start: 0.8068 (tt0) cc_final: 0.7612 (tm-30) REVERT: H 86 MET cc_start: 0.6839 (ptp) cc_final: 0.6633 (ptp) REVERT: M 21 LEU cc_start: 0.7795 (tp) cc_final: 0.7294 (tt) REVERT: M 33 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7816 (m-10) outliers start: 86 outliers final: 67 residues processed: 212 average time/residue: 0.2168 time to fit residues: 69.8385 Evaluate side-chains 206 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 137 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13504 Z= 0.217 Angle : 0.603 9.248 18403 Z= 0.304 Chirality : 0.044 0.162 2089 Planarity : 0.004 0.054 2344 Dihedral : 6.220 82.858 1913 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.35 % Allowed : 19.74 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.59 (0.21), residues: 1681 helix: 2.95 (0.88), residues: 33 sheet: 0.15 (0.19), residues: 719 loop : -0.95 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 39 HIS 0.004 0.001 HIS M 38 PHE 0.027 0.002 PHE C 278 TYR 0.020 0.001 TYR N 50 ARG 0.004 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 159 time to evaluate : 1.663 Fit side-chains REVERT: A 39 ASP cc_start: 0.8421 (p0) cc_final: 0.8050 (p0) REVERT: A 278 PHE cc_start: 0.8692 (p90) cc_final: 0.8253 (p90) REVERT: B 296 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7730 (m-70) REVERT: C 39 ASP cc_start: 0.8573 (p0) cc_final: 0.8268 (p0) REVERT: C 273 TYR cc_start: 0.7573 (m-10) cc_final: 0.7284 (m-10) REVERT: H 8 VAL cc_start: 0.8980 (t) cc_final: 0.8770 (m) REVERT: H 9 GLU cc_start: 0.6275 (mt-10) cc_final: 0.6063 (mt-10) REVERT: H 21 LEU cc_start: 0.7003 (tt) cc_final: 0.6542 (tt) REVERT: L 5 MET cc_start: 0.8391 (tpp) cc_final: 0.8134 (tpp) REVERT: L 82 GLU cc_start: 0.6936 (pm20) cc_final: 0.6577 (pm20) REVERT: M 21 LEU cc_start: 0.7710 (tp) cc_final: 0.6744 (tt) REVERT: M 33 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7875 (m-10) REVERT: N 6 THR cc_start: 0.8843 (t) cc_final: 0.8593 (p) REVERT: N 19 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7754 (ttt-90) REVERT: N 46 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6447 (mmtt) REVERT: N 93 LYS cc_start: 0.8586 (tppt) cc_final: 0.8337 (ttmt) outliers start: 74 outliers final: 59 residues processed: 213 average time/residue: 0.2209 time to fit residues: 72.4264 Evaluate side-chains 211 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 149 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 159 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 160 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13504 Z= 0.221 Angle : 0.606 8.862 18403 Z= 0.303 Chirality : 0.044 0.160 2089 Planarity : 0.004 0.054 2344 Dihedral : 6.086 80.528 1913 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 6.15 % Allowed : 19.31 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.52 (0.21), residues: 1681 helix: 3.36 (0.88), residues: 33 sheet: 0.25 (0.19), residues: 714 loop : -0.96 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 39 HIS 0.003 0.001 HIS M 38 PHE 0.038 0.002 PHE B 278 TYR 0.018 0.001 TYR N 50 ARG 0.004 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 154 time to evaluate : 1.571 Fit side-chains REVERT: A 39 ASP cc_start: 0.8438 (p0) cc_final: 0.8064 (p0) REVERT: A 278 PHE cc_start: 0.8617 (p90) cc_final: 0.8187 (p90) REVERT: C 39 ASP cc_start: 0.8580 (p0) cc_final: 0.8260 (p0) REVERT: C 210 TYR cc_start: 0.8665 (m-80) cc_final: 0.8361 (m-80) REVERT: C 273 TYR cc_start: 0.7624 (m-10) cc_final: 0.7363 (m-10) REVERT: H 9 GLU cc_start: 0.6250 (mt-10) cc_final: 0.6024 (mt-10) REVERT: H 21 LEU cc_start: 0.6905 (tt) cc_final: 0.6263 (tt) REVERT: H 42 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: L 5 MET cc_start: 0.8376 (tpp) cc_final: 0.8136 (tpp) REVERT: L 82 GLU cc_start: 0.6940 (pm20) cc_final: 0.6625 (pm20) REVERT: M 21 LEU cc_start: 0.7423 (tp) cc_final: 0.6745 (tt) REVERT: M 33 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7960 (m-10) REVERT: N 6 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8648 (p) REVERT: N 19 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7556 (ttt-90) REVERT: N 46 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6583 (mtpt) outliers start: 85 outliers final: 65 residues processed: 217 average time/residue: 0.2073 time to fit residues: 70.1859 Evaluate side-chains 213 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 144 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13504 Z= 0.279 Angle : 0.626 9.200 18403 Z= 0.315 Chirality : 0.044 0.162 2089 Planarity : 0.005 0.055 2344 Dihedral : 6.147 77.151 1913 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.93 % Allowed : 19.67 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.55 (0.21), residues: 1681 helix: 3.55 (0.88), residues: 33 sheet: 0.22 (0.19), residues: 718 loop : -0.99 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 39 HIS 0.003 0.001 HIS M 38 PHE 0.037 0.002 PHE B 278 TYR 0.019 0.002 TYR N 50 ARG 0.006 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 154 time to evaluate : 1.665 Fit side-chains REVERT: A 39 ASP cc_start: 0.8467 (p0) cc_final: 0.8090 (p0) REVERT: A 278 PHE cc_start: 0.8709 (p90) cc_final: 0.8268 (p90) REVERT: C 39 ASP cc_start: 0.8589 (p0) cc_final: 0.8294 (p0) REVERT: C 210 TYR cc_start: 0.8686 (m-80) cc_final: 0.8313 (m-80) REVERT: C 273 TYR cc_start: 0.7572 (m-10) cc_final: 0.7215 (m-10) REVERT: D 42 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7977 (tm-30) REVERT: L 5 MET cc_start: 0.8405 (tpp) cc_final: 0.8144 (tpp) REVERT: L 62 ARG cc_start: 0.6391 (ptt90) cc_final: 0.6039 (ptt90) REVERT: L 82 GLU cc_start: 0.6905 (pm20) cc_final: 0.6624 (pm20) REVERT: M 21 LEU cc_start: 0.7154 (tp) cc_final: 0.6845 (tt) REVERT: M 33 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7958 (m-10) REVERT: M 42 GLN cc_start: 0.8251 (tm-30) cc_final: 0.8006 (tm-30) REVERT: N 6 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8625 (p) REVERT: N 19 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7580 (ttt-90) REVERT: N 46 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6711 (mtpt) outliers start: 82 outliers final: 71 residues processed: 213 average time/residue: 0.2063 time to fit residues: 68.1470 Evaluate side-chains 221 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 147 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 140 optimal weight: 0.0020 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13504 Z= 0.167 Angle : 0.584 9.165 18403 Z= 0.289 Chirality : 0.044 0.155 2089 Planarity : 0.004 0.052 2344 Dihedral : 5.869 73.549 1913 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.34 % Allowed : 21.33 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.40 (0.21), residues: 1681 helix: 3.66 (0.88), residues: 33 sheet: 0.35 (0.19), residues: 717 loop : -0.91 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 39 HIS 0.003 0.001 HIS B 211 PHE 0.031 0.001 PHE B 278 TYR 0.018 0.001 TYR N 50 ARG 0.003 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 165 time to evaluate : 1.599 Fit side-chains REVERT: A 39 ASP cc_start: 0.8423 (p0) cc_final: 0.8005 (p0) REVERT: A 278 PHE cc_start: 0.8586 (p90) cc_final: 0.8201 (p90) REVERT: C 39 ASP cc_start: 0.8565 (p0) cc_final: 0.8251 (p0) REVERT: C 210 TYR cc_start: 0.8652 (m-80) cc_final: 0.8269 (m-80) REVERT: C 273 TYR cc_start: 0.7574 (m-10) cc_final: 0.7287 (m-10) REVERT: D 41 ARG cc_start: 0.8184 (ptm-80) cc_final: 0.7723 (ptt90) REVERT: D 42 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7848 (tm-30) REVERT: L 5 MET cc_start: 0.8173 (tpp) cc_final: 0.7964 (tpp) REVERT: L 28 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7954 (tm-30) REVERT: L 82 GLU cc_start: 0.6843 (pm20) cc_final: 0.6586 (pm20) REVERT: M 21 LEU cc_start: 0.7074 (tp) cc_final: 0.6772 (tt) REVERT: M 42 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7969 (tm-30) REVERT: N 6 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8634 (p) REVERT: N 28 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7751 (tm-30) REVERT: N 46 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6377 (mmtt) outliers start: 60 outliers final: 49 residues processed: 208 average time/residue: 0.2157 time to fit residues: 68.9506 Evaluate side-chains 205 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 0.037 13504 Z= 0.204 Angle : 0.613 9.294 18403 Z= 0.302 Chirality : 0.044 0.164 2089 Planarity : 0.004 0.056 2344 Dihedral : 5.853 70.670 1913 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.12 % Allowed : 21.69 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.36 (0.21), residues: 1681 helix: 3.77 (0.88), residues: 33 sheet: 0.44 (0.20), residues: 707 loop : -0.93 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.003 0.001 HIS M 38 PHE 0.032 0.002 PHE B 278 TYR 0.023 0.001 TYR M 33 ARG 0.003 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 163 time to evaluate : 1.575 Fit side-chains REVERT: A 39 ASP cc_start: 0.8411 (p0) cc_final: 0.8066 (p0) REVERT: A 278 PHE cc_start: 0.8598 (p90) cc_final: 0.8191 (p90) REVERT: B 85 TYR cc_start: 0.6360 (t80) cc_final: 0.5795 (t80) REVERT: C 39 ASP cc_start: 0.8595 (p0) cc_final: 0.8291 (p0) REVERT: C 210 TYR cc_start: 0.8661 (m-80) cc_final: 0.8282 (m-80) REVERT: C 273 TYR cc_start: 0.7530 (m-10) cc_final: 0.7188 (m-10) REVERT: D 42 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7917 (tm-30) REVERT: H 42 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: L 5 MET cc_start: 0.8203 (tpp) cc_final: 0.7999 (tpp) REVERT: L 62 ARG cc_start: 0.6647 (ptt90) cc_final: 0.6265 (ptt90) REVERT: L 82 GLU cc_start: 0.6987 (pm20) cc_final: 0.6726 (pm20) REVERT: M 21 LEU cc_start: 0.7283 (tp) cc_final: 0.6713 (tt) REVERT: M 42 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8102 (tm-30) REVERT: N 6 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8683 (p) REVERT: N 46 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6541 (mmtm) outliers start: 57 outliers final: 52 residues processed: 204 average time/residue: 0.2017 time to fit residues: 64.1725 Evaluate side-chains 211 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 156 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 131 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135737 restraints weight = 22094.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134777 restraints weight = 29983.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136193 restraints weight = 26418.016| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13504 Z= 0.315 Angle : 0.660 9.361 18403 Z= 0.332 Chirality : 0.045 0.200 2089 Planarity : 0.005 0.056 2344 Dihedral : 6.054 67.531 1913 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.41 % Allowed : 21.76 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.54 (0.21), residues: 1681 helix: 3.84 (0.88), residues: 33 sheet: 0.31 (0.20), residues: 718 loop : -1.07 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 39 HIS 0.004 0.001 HIS M 38 PHE 0.044 0.002 PHE C 278 TYR 0.028 0.002 TYR M 33 ARG 0.005 0.000 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.44 seconds wall clock time: 47 minutes 42.30 seconds (2862.30 seconds total)