Starting phenix.real_space_refine on Thu Feb 15 04:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6za9_11127/02_2024/6za9_11127_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6za9_11127/02_2024/6za9_11127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6za9_11127/02_2024/6za9_11127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6za9_11127/02_2024/6za9_11127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6za9_11127/02_2024/6za9_11127_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6za9_11127/02_2024/6za9_11127_updated.pdb" } resolution = 3.76 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= 0.008 sd= 0.031 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 13 5.49 5 S 53 5.16 5 C 7370 2.51 5 N 1676 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 38": "NH1" <-> "NH2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "7 ARG 38": "NH1" <-> "NH2" Residue "8 ARG 38": "NH1" <-> "NH2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "M PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "N ARG 41": "NH1" <-> "NH2" Residue "N ARG 159": "NH1" <-> "NH2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "R ARG 85": "NH1" <-> "NH2" Residue "T ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11067 Number of models: 1 Model: "" Number of chains: 23 Chain: "1" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "2" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "3" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "4" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "5" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "6" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "7" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "8" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "K" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "M" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 519 Classifications: {'peptide': 60} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1734 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "O" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "P" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Q" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 701 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "S" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 673 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "2" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "N" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 92 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 237 Unusual residues: {'CDL': 2, 'LHG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "S" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Classifications: {'peptide': 1} Time building chain proxies: 5.97, per 1000 atoms: 0.54 Number of scatterers: 11067 At special positions: 0 Unit cell: (109.283, 127.32, 132.625, 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 53 16.00 P 13 15.00 O 1955 8.00 N 1676 7.00 C 7370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.9 seconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain '1' and resid 2 through 13 Processing helix chain '1' and resid 16 through 36 removed outlier: 3.656A pdb=" N ALA 1 23 " --> pdb=" O GLY 1 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE 1 25 " --> pdb=" O GLY 1 22 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE 1 29 " --> pdb=" O GLY 1 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY 1 30 " --> pdb=" O THR 1 27 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE 1 34 " --> pdb=" O SER 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 72 removed outlier: 5.849A pdb=" N GLN 1 44 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN 1 45 " --> pdb=" O LEU 1 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU 1 46 " --> pdb=" O LYS 1 43 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU 1 62 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 38 removed outlier: 3.848A pdb=" N THR 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL 2 16 " --> pdb=" O GLY 2 12 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL 2 18 " --> pdb=" O ALA 2 14 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA 2 19 " --> pdb=" O THR 2 15 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG 2 38 " --> pdb=" O ILE 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 72 Processing helix chain '3' and resid 2 through 13 Processing helix chain '3' and resid 16 through 38 removed outlier: 3.506A pdb=" N GLY 3 20 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA 3 23 " --> pdb=" O GLY 3 20 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE 3 25 " --> pdb=" O GLY 3 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY 3 26 " --> pdb=" O ALA 3 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 3 29 " --> pdb=" O GLY 3 26 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY 3 30 " --> pdb=" O THR 3 27 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE 3 34 " --> pdb=" O SER 3 31 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR 3 36 " --> pdb=" O ILE 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 72 removed outlier: 3.669A pdb=" N LYS 3 43 " --> pdb=" O PRO 3 40 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN 3 44 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN 3 45 " --> pdb=" O LEU 3 42 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU 3 46 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU 3 58 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS 3 64 " --> pdb=" O GLY 3 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 3 65 " --> pdb=" O LEU 3 62 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 13 Processing helix chain '4' and resid 16 through 36 removed outlier: 3.601A pdb=" N ALA 4 23 " --> pdb=" O GLY 4 20 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE 4 25 " --> pdb=" O GLY 4 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE 4 29 " --> pdb=" O GLY 4 26 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE 4 34 " --> pdb=" O SER 4 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR 4 36 " --> pdb=" O ILE 4 33 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 73 removed outlier: 3.601A pdb=" N LYS 4 43 " --> pdb=" O PRO 4 40 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN 4 44 " --> pdb=" O SER 4 41 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN 4 45 " --> pdb=" O LEU 4 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE 4 69 " --> pdb=" O MET 4 66 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE 4 73 " --> pdb=" O LEU 4 70 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 13 Processing helix chain '5' and resid 16 through 36 removed outlier: 3.753A pdb=" N GLY 5 20 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 5 23 " --> pdb=" O GLY 5 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE 5 25 " --> pdb=" O GLY 5 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY 5 26 " --> pdb=" O ALA 5 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE 5 29 " --> pdb=" O GLY 5 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 5 30 " --> pdb=" O THR 5 27 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE 5 34 " --> pdb=" O SER 5 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR 5 36 " --> pdb=" O ILE 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 72 Processing helix chain '6' and resid 2 through 13 Processing helix chain '6' and resid 16 through 36 removed outlier: 4.336A pdb=" N GLY 6 20 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA 6 23 " --> pdb=" O GLY 6 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE 6 25 " --> pdb=" O GLY 6 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE 6 29 " --> pdb=" O GLY 6 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE 6 34 " --> pdb=" O SER 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 72 removed outlier: 3.725A pdb=" N LYS 6 43 " --> pdb=" O PRO 6 40 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN 6 44 " --> pdb=" O SER 6 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU 6 46 " --> pdb=" O LYS 6 43 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER 6 57 " --> pdb=" O PHE 6 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU 6 62 " --> pdb=" O ALA 6 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU 6 65 " --> pdb=" O LEU 6 62 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 36 removed outlier: 3.724A pdb=" N THR 7 15 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL 7 16 " --> pdb=" O GLY 7 12 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL 7 18 " --> pdb=" O ALA 7 14 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Processing helix chain '8' and resid 2 through 13 Processing helix chain '8' and resid 16 through 38 removed outlier: 3.629A pdb=" N ALA 8 23 " --> pdb=" O GLY 8 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 8 25 " --> pdb=" O GLY 8 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE 8 29 " --> pdb=" O GLY 8 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY 8 30 " --> pdb=" O THR 8 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE 8 34 " --> pdb=" O SER 8 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR 8 36 " --> pdb=" O ILE 8 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG 8 38 " --> pdb=" O GLY 8 35 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 72 removed outlier: 3.768A pdb=" N LYS 8 43 " --> pdb=" O PRO 8 40 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN 8 44 " --> pdb=" O SER 8 41 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN 8 45 " --> pdb=" O LEU 8 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU 8 46 " --> pdb=" O LYS 8 43 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE 8 54 " --> pdb=" O ILE 8 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 8 62 " --> pdb=" O ALA 8 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 8 65 " --> pdb=" O LEU 8 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 29 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 45 Processing helix chain 'K' and resid 56 through 72 Processing helix chain 'K' and resid 76 through 118 removed outlier: 3.536A pdb=" N LEU K 85 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 123 Processing helix chain 'M' and resid 134 through 139 Processing helix chain 'M' and resid 141 through 143 No H-bonds generated for 'chain 'M' and resid 141 through 143' Processing helix chain 'N' and resid 19 through 28 Proline residue: N 27 - end of helix Processing helix chain 'N' and resid 41 through 57 Processing helix chain 'N' and resid 64 through 86 Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 98 through 119 Proline residue: N 107 - end of helix Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'N' and resid 135 through 149 Proline residue: N 139 - end of helix removed outlier: 3.729A pdb=" N ILE N 147 " --> pdb=" O ILE N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 184 Processing helix chain 'N' and resid 186 through 225 removed outlier: 4.153A pdb=" N ASN N 225 " --> pdb=" O TYR N 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 48 Processing helix chain 'P' and resid 2 through 8 Processing helix chain 'P' and resid 14 through 17 No H-bonds generated for 'chain 'P' and resid 14 through 17' Processing helix chain 'P' and resid 22 through 51 Processing helix chain 'Q' and resid 2 through 4 No H-bonds generated for 'chain 'Q' and resid 2 through 4' Processing helix chain 'Q' and resid 9 through 17 Processing helix chain 'Q' and resid 22 through 29 Processing helix chain 'R' and resid 12 through 14 No H-bonds generated for 'chain 'R' and resid 12 through 14' Processing helix chain 'R' and resid 20 through 26 Processing helix chain 'R' and resid 31 through 49 Processing helix chain 'R' and resid 58 through 82 removed outlier: 3.563A pdb=" N LYS R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS R 81 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 37 Proline residue: S 25 - end of helix removed outlier: 3.829A pdb=" N TYR S 33 " --> pdb=" O THR S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 61 Processing helix chain 'S' and resid 70 through 95 Processing helix chain 'T' and resid 9 through 69 Proline residue: T 35 - end of helix 772 hydrogen bonds defined for protein. 1704 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: 2.89 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1729 1.32 - 1.45: 2879 1.45 - 1.57: 6544 1.57 - 1.69: 26 1.69 - 1.82: 95 Bond restraints: 11273 Sorted by residual: bond pdb=" C13 S12 T 201 " pdb=" C14 S12 T 201 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C38 CDL R 301 " pdb=" C39 CDL R 301 " ideal model delta sigma weight residual 1.517 1.313 0.204 2.70e-02 1.37e+03 5.73e+01 bond pdb=" C61 CDL R 302 " pdb=" C62 CDL R 302 " ideal model delta sigma weight residual 1.517 1.314 0.203 2.70e-02 1.37e+03 5.67e+01 bond pdb=" C41 CDL R 301 " pdb=" C42 CDL R 301 " ideal model delta sigma weight residual 1.517 1.315 0.202 2.70e-02 1.37e+03 5.62e+01 bond pdb=" C58 CDL N 401 " pdb=" C59 CDL N 401 " ideal model delta sigma weight residual 1.517 1.315 0.202 2.70e-02 1.37e+03 5.59e+01 ... (remaining 11268 not shown) Histogram of bond angle deviations from ideal: 94.22 - 102.20: 61 102.20 - 110.18: 2285 110.18 - 118.16: 6236 118.16 - 126.14: 6380 126.14 - 134.12: 154 Bond angle restraints: 15116 Sorted by residual: angle pdb=" CB3 CDL R 301 " pdb=" OB5 CDL R 301 " pdb=" PB2 CDL R 301 " ideal model delta sigma weight residual 121.27 129.03 -7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" CA3 CDL N 401 " pdb=" OA5 CDL N 401 " pdb=" PA1 CDL N 401 " ideal model delta sigma weight residual 121.27 128.13 -6.86 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA2 CDL R 301 " pdb=" OA2 CDL R 301 " pdb=" PA1 CDL R 301 " ideal model delta sigma weight residual 121.27 128.07 -6.80 1.00e+00 1.00e+00 4.62e+01 angle pdb=" CB3 CDL N 401 " pdb=" OB5 CDL N 401 " pdb=" PB2 CDL N 401 " ideal model delta sigma weight residual 121.27 127.27 -6.00 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA3 CDL R 302 " pdb=" OA5 CDL R 302 " pdb=" PA1 CDL R 302 " ideal model delta sigma weight residual 121.27 127.09 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 15111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 6447 33.44 - 66.88: 350 66.88 - 100.32: 7 100.32 - 133.76: 1 133.76 - 167.20: 1 Dihedral angle restraints: 6806 sinusoidal: 2904 harmonic: 3902 Sorted by residual: dihedral pdb=" CA GLY O 14 " pdb=" C GLY O 14 " pdb=" N ILE O 15 " pdb=" CA ILE O 15 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE N 147 " pdb=" C ILE N 147 " pdb=" N SER N 148 " pdb=" CA SER N 148 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA MET Q 40 " pdb=" C MET Q 40 " pdb=" N THR Q 41 " pdb=" CA THR Q 41 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 1708 1.018 - 2.035: 0 2.035 - 3.053: 0 3.053 - 4.071: 0 4.071 - 5.088: 4 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CB4 CDL R 301 " pdb=" CB3 CDL R 301 " pdb=" CB6 CDL R 301 " pdb=" OB6 CDL R 301 " both_signs ideal model delta sigma weight residual False -2.57 2.51 -5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" CB4 CDL N 401 " pdb=" CB3 CDL N 401 " pdb=" CB6 CDL N 401 " pdb=" OB6 CDL N 401 " both_signs ideal model delta sigma weight residual False -2.57 2.37 -4.95 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" CB4 CDL R 302 " pdb=" CB3 CDL R 302 " pdb=" CB6 CDL R 302 " pdb=" OB6 CDL R 302 " both_signs ideal model delta sigma weight residual False -2.57 2.15 -4.72 2.00e-01 2.50e+01 5.57e+02 ... (remaining 1709 not shown) Planarity restraints: 1807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 S12 T 201 " -0.132 2.00e-02 2.50e+03 2.27e-01 5.17e+02 pdb=" C13 S12 T 201 " 0.293 2.00e-02 2.50e+03 pdb=" C14 S12 T 201 " -0.293 2.00e-02 2.50e+03 pdb=" C15 S12 T 201 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG K 301 " 0.127 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C8 LHG K 301 " -0.037 2.00e-02 2.50e+03 pdb=" O7 LHG K 301 " -0.039 2.00e-02 2.50e+03 pdb=" O9 LHG K 301 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG 2 101 " 0.102 2.00e-02 2.50e+03 5.89e-02 3.46e+01 pdb=" C8 LHG 2 101 " -0.030 2.00e-02 2.50e+03 pdb=" O7 LHG 2 101 " -0.031 2.00e-02 2.50e+03 pdb=" O9 LHG 2 101 " -0.041 2.00e-02 2.50e+03 ... (remaining 1804 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2608 2.78 - 3.31: 10550 3.31 - 3.84: 18852 3.84 - 4.37: 21173 4.37 - 4.90: 36195 Nonbonded interactions: 89378 Sorted by model distance: nonbonded pdb=" O GLY N 111 " pdb=" OG1 THR N 115 " model vdw 2.254 2.440 nonbonded pdb=" O2 LHG S 202 " pdb=" O3 LHG S 202 " model vdw 2.264 2.432 nonbonded pdb=" OH TYR K 26 " pdb=" O PRO T 3 " model vdw 2.283 2.440 nonbonded pdb=" O ASN S 58 " pdb=" OG1 THR S 62 " model vdw 2.290 2.440 nonbonded pdb=" O6 LHG S 201 " pdb=" O7 LHG S 201 " model vdw 2.292 2.432 ... (remaining 89373 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 '1' selection = (chain '2' and resid 1 through 74) selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } 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: 0.050 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: 1.060 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 30.040 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.204 11273 Z= 0.737 Angle : 1.529 13.701 15116 Z= 0.700 Chirality : 0.242 5.088 1712 Planarity : 0.010 0.227 1807 Dihedral : 17.109 167.204 4316 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.74 % Allowed : 8.24 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.17), residues: 1340 helix: -2.04 (0.12), residues: 1047 sheet: None (None), residues: 0 loop : -3.07 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.005 TRP Q 9 HIS 0.009 0.002 HIS N 168 PHE 0.031 0.003 PHE 8 63 TYR 0.031 0.003 TYR R 72 ARG 0.010 0.001 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 331 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: 3 43 LYS cc_start: 0.8112 (tttt) cc_final: 0.7475 (ttpp) REVERT: 3 66 MET cc_start: 0.6756 (ttp) cc_final: 0.5505 (tpt) REVERT: 4 66 MET cc_start: 0.6587 (pp-130) cc_final: 0.4831 (mmm) REVERT: 6 47 PHE cc_start: 0.8397 (t80) cc_final: 0.7957 (t80) REVERT: 6 66 MET cc_start: 0.7776 (ttp) cc_final: 0.7571 (ttt) REVERT: 6 69 PHE cc_start: 0.8010 (m-10) cc_final: 0.7744 (t80) REVERT: 7 43 LYS cc_start: 0.7320 (tttt) cc_final: 0.7112 (tttt) REVERT: 7 47 PHE cc_start: 0.8605 (t80) cc_final: 0.8351 (t80) REVERT: 7 51 ILE cc_start: 0.8203 (tp) cc_final: 0.7940 (tt) REVERT: K 44 TYR cc_start: 0.9152 (t80) cc_final: 0.8889 (t80) REVERT: K 114 GLN cc_start: 0.6863 (mt0) cc_final: 0.6508 (mm-40) REVERT: M 109 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7927 (mttt) REVERT: M 121 LYS cc_start: 0.8175 (tmmt) cc_final: 0.7853 (tttt) REVERT: M 138 GLU cc_start: 0.8843 (tt0) cc_final: 0.8344 (tm-30) REVERT: M 152 TYR cc_start: 0.8943 (m-80) cc_final: 0.8581 (m-80) REVERT: N 35 ASN cc_start: 0.9039 (m110) cc_final: 0.8466 (p0) REVERT: N 140 MET cc_start: 0.8906 (tmm) cc_final: 0.8656 (tmm) REVERT: N 194 ILE cc_start: 0.9148 (mm) cc_final: 0.8941 (mt) REVERT: O 35 TYR cc_start: 0.7919 (m-10) cc_final: 0.7673 (m-10) REVERT: R 19 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8053 (tp30) REVERT: R 62 MET cc_start: 0.9191 (mtt) cc_final: 0.8910 (mtp) REVERT: S 35 LYS cc_start: 0.9026 (tmtp) cc_final: 0.8353 (mttt) REVERT: S 66 LYS cc_start: 0.8828 (pttt) cc_final: 0.8578 (ptmm) REVERT: S 85 MET cc_start: 0.8746 (mmt) cc_final: 0.8453 (mmm) REVERT: S 96 ARG cc_start: 0.9215 (mtm-85) cc_final: 0.7217 (tpm170) outliers start: 8 outliers final: 1 residues processed: 337 average time/residue: 0.2393 time to fit residues: 111.2560 Evaluate side-chains 241 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.0030 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 39 ASN 5 39 ASN 7 39 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11273 Z= 0.254 Angle : 0.695 13.985 15116 Z= 0.361 Chirality : 0.040 0.193 1712 Planarity : 0.006 0.050 1807 Dihedral : 17.137 167.154 1994 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.63 % Allowed : 15.74 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1340 helix: -0.28 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -2.51 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 9 HIS 0.003 0.001 HIS N 168 PHE 0.024 0.002 PHE K 24 TYR 0.029 0.002 TYR M 150 ARG 0.006 0.001 ARG T 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: 3 66 MET cc_start: 0.6156 (ttp) cc_final: 0.5267 (tpt) REVERT: 6 47 PHE cc_start: 0.8436 (t80) cc_final: 0.8028 (t80) REVERT: 6 66 MET cc_start: 0.7557 (ttp) cc_final: 0.7329 (ttt) REVERT: 7 47 PHE cc_start: 0.8647 (t80) cc_final: 0.8359 (t80) REVERT: 7 51 ILE cc_start: 0.8115 (tp) cc_final: 0.7719 (tt) REVERT: K 16 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8755 (pp) REVERT: K 87 GLU cc_start: 0.8686 (tt0) cc_final: 0.8438 (mt-10) REVERT: K 114 GLN cc_start: 0.6750 (mt0) cc_final: 0.6281 (tt0) REVERT: M 109 LYS cc_start: 0.8494 (mmmt) cc_final: 0.7931 (mttt) REVERT: M 138 GLU cc_start: 0.8844 (tt0) cc_final: 0.8397 (tm-30) REVERT: M 139 VAL cc_start: 0.8599 (p) cc_final: 0.8361 (t) REVERT: N 14 MET cc_start: 0.8503 (tpp) cc_final: 0.7877 (tpp) REVERT: N 35 ASN cc_start: 0.9056 (m110) cc_final: 0.8400 (p0) REVERT: N 46 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7034 (mt0) REVERT: N 140 MET cc_start: 0.8804 (tmm) cc_final: 0.8578 (tmm) REVERT: N 163 ASN cc_start: 0.8480 (m-40) cc_final: 0.8273 (t0) REVERT: Q 12 MET cc_start: 0.8247 (tpp) cc_final: 0.7971 (tpp) REVERT: Q 20 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9078 (tp) REVERT: S 35 LYS cc_start: 0.9048 (tmtp) cc_final: 0.8461 (mttt) REVERT: S 85 MET cc_start: 0.8780 (mmt) cc_final: 0.8403 (mmm) outliers start: 50 outliers final: 23 residues processed: 299 average time/residue: 0.1995 time to fit residues: 87.0342 Evaluate side-chains 263 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 237 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 overall best weight: 1.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 45 GLN 7 39 ASN ** 8 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11273 Z= 0.181 Angle : 0.622 11.528 15116 Z= 0.316 Chirality : 0.038 0.202 1712 Planarity : 0.005 0.052 1807 Dihedral : 16.118 162.225 1994 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.17 % Allowed : 18.70 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1340 helix: 0.16 (0.15), residues: 1044 sheet: None (None), residues: 0 loop : -2.28 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 9 HIS 0.003 0.001 HIS N 168 PHE 0.015 0.001 PHE 8 54 TYR 0.021 0.001 TYR R 72 ARG 0.004 0.000 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 1.213 Fit side-chains REVERT: 1 63 PHE cc_start: 0.7856 (t80) cc_final: 0.7600 (t80) REVERT: 3 66 MET cc_start: 0.6001 (ttp) cc_final: 0.5192 (tpt) REVERT: 6 47 PHE cc_start: 0.8499 (t80) cc_final: 0.8012 (t80) REVERT: 6 66 MET cc_start: 0.7391 (ttp) cc_final: 0.7185 (ttt) REVERT: 7 47 PHE cc_start: 0.8650 (t80) cc_final: 0.8379 (t80) REVERT: 7 51 ILE cc_start: 0.8138 (tp) cc_final: 0.7771 (tt) REVERT: 7 66 MET cc_start: 0.7715 (tmm) cc_final: 0.7421 (tmm) REVERT: 7 71 ILE cc_start: 0.8359 (tt) cc_final: 0.8124 (tt) REVERT: K 28 LYS cc_start: 0.8557 (mptm) cc_final: 0.8224 (mttm) REVERT: K 87 GLU cc_start: 0.8641 (tt0) cc_final: 0.8412 (mt-10) REVERT: K 114 GLN cc_start: 0.6698 (mt0) cc_final: 0.6430 (mm-40) REVERT: M 108 SER cc_start: 0.7433 (m) cc_final: 0.7163 (t) REVERT: M 109 LYS cc_start: 0.8506 (mmmt) cc_final: 0.7938 (mttt) REVERT: M 138 GLU cc_start: 0.8820 (tt0) cc_final: 0.8380 (tm-30) REVERT: M 152 TYR cc_start: 0.8969 (m-80) cc_final: 0.8541 (m-80) REVERT: N 14 MET cc_start: 0.8370 (tpp) cc_final: 0.7787 (tpp) REVERT: N 35 ASN cc_start: 0.9015 (m110) cc_final: 0.8415 (p0) REVERT: N 46 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.6932 (mt0) REVERT: N 71 MET cc_start: 0.8782 (tmm) cc_final: 0.8087 (tmm) REVERT: N 131 GLN cc_start: 0.8665 (pm20) cc_final: 0.8083 (mt0) REVERT: Q 20 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9100 (tp) REVERT: S 32 TYR cc_start: 0.8135 (t80) cc_final: 0.7890 (t80) REVERT: S 35 LYS cc_start: 0.8915 (tmtp) cc_final: 0.8384 (mttt) REVERT: T 16 TYR cc_start: 0.8295 (m-10) cc_final: 0.7821 (m-10) REVERT: T 70 LEU cc_start: 0.3316 (OUTLIER) cc_final: 0.2890 (mt) outliers start: 45 outliers final: 24 residues processed: 294 average time/residue: 0.2099 time to fit residues: 88.7727 Evaluate side-chains 266 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 ASN N 163 ASN N 210 GLN Q 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11273 Z= 0.229 Angle : 0.632 11.073 15116 Z= 0.320 Chirality : 0.039 0.196 1712 Planarity : 0.005 0.051 1807 Dihedral : 15.403 159.196 1994 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.37 % Allowed : 21.48 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1340 helix: 0.33 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -2.20 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 25 HIS 0.004 0.001 HIS N 168 PHE 0.025 0.001 PHE K 24 TYR 0.022 0.001 TYR R 72 ARG 0.007 0.001 ARG M 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 58 GLU cc_start: 0.7950 (tp30) cc_final: 0.7680 (tp30) REVERT: 1 63 PHE cc_start: 0.7670 (t80) cc_final: 0.7418 (t80) REVERT: 2 60 MET cc_start: 0.6425 (mmm) cc_final: 0.6133 (mmp) REVERT: 3 66 MET cc_start: 0.6248 (ttp) cc_final: 0.5176 (tpt) REVERT: 5 39 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8436 (p0) REVERT: 6 47 PHE cc_start: 0.8472 (t80) cc_final: 0.7986 (t80) REVERT: 7 47 PHE cc_start: 0.8651 (t80) cc_final: 0.8421 (t80) REVERT: 7 51 ILE cc_start: 0.8169 (tp) cc_final: 0.7750 (tt) REVERT: 7 71 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8181 (tt) REVERT: K 28 LYS cc_start: 0.8652 (mptm) cc_final: 0.8302 (mttm) REVERT: K 87 GLU cc_start: 0.8636 (tt0) cc_final: 0.8417 (mt-10) REVERT: K 114 GLN cc_start: 0.6674 (mt0) cc_final: 0.6456 (mm-40) REVERT: M 138 GLU cc_start: 0.8823 (tt0) cc_final: 0.8390 (tm-30) REVERT: M 152 TYR cc_start: 0.8975 (m-80) cc_final: 0.8533 (m-80) REVERT: N 46 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: N 149 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8561 (tp) REVERT: N 209 ILE cc_start: 0.9037 (mt) cc_final: 0.8833 (mt) REVERT: R 14 GLU cc_start: 0.7939 (tp30) cc_final: 0.7365 (tm-30) REVERT: S 86 TRP cc_start: 0.7826 (OUTLIER) cc_final: 0.6193 (m-90) REVERT: T 51 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6006 (ppp-140) outliers start: 58 outliers final: 34 residues processed: 290 average time/residue: 0.2039 time to fit residues: 86.3262 Evaluate side-chains 284 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 244 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 39 ASN Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 8 residue 49 TYR Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 31 optimal weight: 0.0870 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11273 Z= 0.190 Angle : 0.606 9.813 15116 Z= 0.304 Chirality : 0.038 0.183 1712 Planarity : 0.005 0.053 1807 Dihedral : 14.813 134.414 1994 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.54 % Allowed : 22.87 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1340 helix: 0.49 (0.16), residues: 1049 sheet: None (None), residues: 0 loop : -1.92 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 25 HIS 0.003 0.001 HIS N 61 PHE 0.015 0.001 PHE 2 29 TYR 0.020 0.001 TYR R 72 ARG 0.004 0.000 ARG M 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 63 PHE cc_start: 0.7638 (t80) cc_final: 0.7395 (t80) REVERT: 2 46 LEU cc_start: 0.6863 (mp) cc_final: 0.6505 (mt) REVERT: 2 72 LEU cc_start: 0.8333 (tp) cc_final: 0.8009 (tp) REVERT: 3 66 MET cc_start: 0.6321 (ttp) cc_final: 0.5245 (tpt) REVERT: 6 47 PHE cc_start: 0.8417 (t80) cc_final: 0.7942 (t80) REVERT: 7 47 PHE cc_start: 0.8641 (t80) cc_final: 0.8418 (t80) REVERT: 7 51 ILE cc_start: 0.8137 (tp) cc_final: 0.7714 (tt) REVERT: 7 71 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (tt) REVERT: K 28 LYS cc_start: 0.8643 (mptm) cc_final: 0.7880 (mmmt) REVERT: K 87 GLU cc_start: 0.8648 (tt0) cc_final: 0.8431 (mt-10) REVERT: K 114 GLN cc_start: 0.6736 (mt0) cc_final: 0.6451 (mm-40) REVERT: M 138 GLU cc_start: 0.8817 (tt0) cc_final: 0.8410 (tm-30) REVERT: M 152 TYR cc_start: 0.8922 (m-80) cc_final: 0.8566 (m-80) REVERT: N 46 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: N 71 MET cc_start: 0.8819 (tmm) cc_final: 0.8143 (tmm) REVERT: N 131 GLN cc_start: 0.8690 (pm20) cc_final: 0.8092 (tt0) REVERT: N 149 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8466 (tp) REVERT: Q 12 MET cc_start: 0.8080 (tpp) cc_final: 0.7864 (tpp) REVERT: R 8 LYS cc_start: 0.8532 (mptt) cc_final: 0.8109 (mmtm) REVERT: R 14 GLU cc_start: 0.7964 (tp30) cc_final: 0.7752 (tp30) REVERT: S 54 LYS cc_start: 0.7635 (mttp) cc_final: 0.7400 (mtmt) REVERT: S 86 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.6306 (m-90) REVERT: T 51 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.5996 (ppp-140) outliers start: 49 outliers final: 28 residues processed: 284 average time/residue: 0.2093 time to fit residues: 85.4279 Evaluate side-chains 279 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 34 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 8 residue 34 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11273 Z= 0.224 Angle : 0.616 9.091 15116 Z= 0.311 Chirality : 0.039 0.183 1712 Planarity : 0.005 0.054 1807 Dihedral : 14.541 127.550 1994 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.46 % Allowed : 23.24 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1340 helix: 0.54 (0.16), residues: 1055 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 25 HIS 0.006 0.001 HIS N 61 PHE 0.019 0.001 PHE 8 54 TYR 0.022 0.001 TYR R 72 ARG 0.003 0.000 ARG S 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 253 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: 1 63 PHE cc_start: 0.7669 (t80) cc_final: 0.7429 (t80) REVERT: 2 46 LEU cc_start: 0.6953 (mp) cc_final: 0.6648 (mt) REVERT: 3 51 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5902 (tp) REVERT: 3 66 MET cc_start: 0.6343 (ttp) cc_final: 0.5268 (tpt) REVERT: 6 47 PHE cc_start: 0.8429 (t80) cc_final: 0.7947 (t80) REVERT: 7 51 ILE cc_start: 0.8138 (tp) cc_final: 0.7880 (tp) REVERT: 7 71 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8159 (tt) REVERT: K 19 GLU cc_start: 0.8663 (tp30) cc_final: 0.8373 (tp30) REVERT: K 87 GLU cc_start: 0.8700 (tt0) cc_final: 0.8442 (mt-10) REVERT: K 114 GLN cc_start: 0.6728 (mt0) cc_final: 0.6485 (mm-40) REVERT: M 138 GLU cc_start: 0.8865 (tt0) cc_final: 0.8482 (tm-30) REVERT: M 152 TYR cc_start: 0.8947 (m-80) cc_final: 0.8577 (m-80) REVERT: N 46 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.6874 (mt0) REVERT: N 71 MET cc_start: 0.8843 (tmm) cc_final: 0.8146 (tmm) REVERT: N 131 GLN cc_start: 0.8684 (pm20) cc_final: 0.8051 (tt0) REVERT: N 149 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8583 (tp) REVERT: Q 12 MET cc_start: 0.8129 (tpp) cc_final: 0.7880 (tpp) REVERT: R 8 LYS cc_start: 0.8539 (mptt) cc_final: 0.8200 (mmtm) REVERT: R 14 GLU cc_start: 0.8082 (tp30) cc_final: 0.7842 (tp30) REVERT: R 46 TYR cc_start: 0.8534 (t80) cc_final: 0.8160 (t80) REVERT: S 86 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.6176 (m-90) REVERT: T 51 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5989 (ppp-140) outliers start: 59 outliers final: 39 residues processed: 290 average time/residue: 0.2083 time to fit residues: 87.5370 Evaluate side-chains 287 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 242 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 67 VAL Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 34 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11273 Z= 0.198 Angle : 0.602 7.956 15116 Z= 0.303 Chirality : 0.038 0.182 1712 Planarity : 0.005 0.054 1807 Dihedral : 14.287 122.309 1994 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.19 % Allowed : 24.07 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1340 helix: 0.58 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.63 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 25 HIS 0.003 0.001 HIS N 168 PHE 0.018 0.001 PHE 7 54 TYR 0.021 0.001 TYR R 72 ARG 0.005 0.000 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 244 time to evaluate : 1.177 Fit side-chains REVERT: 1 60 MET cc_start: 0.7503 (tpp) cc_final: 0.7118 (tpp) REVERT: 1 63 PHE cc_start: 0.7643 (t80) cc_final: 0.7407 (t80) REVERT: 2 46 LEU cc_start: 0.6981 (mp) cc_final: 0.6616 (mt) REVERT: 2 72 LEU cc_start: 0.8337 (tp) cc_final: 0.8018 (tp) REVERT: 3 51 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5885 (tp) REVERT: 3 66 MET cc_start: 0.6445 (ttp) cc_final: 0.5352 (tpt) REVERT: 5 39 ASN cc_start: 0.8727 (p0) cc_final: 0.8384 (p0) REVERT: 6 47 PHE cc_start: 0.8405 (t80) cc_final: 0.7948 (t80) REVERT: 7 51 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7893 (tp) REVERT: 7 71 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8142 (tt) REVERT: 8 62 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8006 (tt) REVERT: K 19 GLU cc_start: 0.8700 (tp30) cc_final: 0.8416 (tp30) REVERT: K 87 GLU cc_start: 0.8683 (tt0) cc_final: 0.8435 (mt-10) REVERT: K 114 GLN cc_start: 0.6811 (mt0) cc_final: 0.6457 (mm-40) REVERT: M 138 GLU cc_start: 0.8827 (tt0) cc_final: 0.8459 (tm-30) REVERT: M 152 TYR cc_start: 0.8919 (m-80) cc_final: 0.8637 (m-80) REVERT: N 46 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: N 131 GLN cc_start: 0.8646 (pm20) cc_final: 0.8070 (tt0) REVERT: N 149 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8511 (tp) REVERT: Q 4 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8547 (mt) REVERT: Q 12 MET cc_start: 0.8116 (tpp) cc_final: 0.7846 (tpp) REVERT: R 8 LYS cc_start: 0.8515 (mptt) cc_final: 0.8219 (mmtm) REVERT: R 14 GLU cc_start: 0.8066 (tp30) cc_final: 0.7766 (tp30) REVERT: R 46 TYR cc_start: 0.8506 (t80) cc_final: 0.8174 (t80) REVERT: S 86 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.6273 (m-90) outliers start: 56 outliers final: 36 residues processed: 279 average time/residue: 0.2181 time to fit residues: 89.1018 Evaluate side-chains 279 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 34 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 8 residue 62 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 86 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11273 Z= 0.236 Angle : 0.627 9.401 15116 Z= 0.314 Chirality : 0.039 0.182 1712 Planarity : 0.005 0.055 1807 Dihedral : 14.190 119.762 1994 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.56 % Allowed : 23.98 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1340 helix: 0.60 (0.16), residues: 1054 sheet: None (None), residues: 0 loop : -1.73 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 25 HIS 0.003 0.001 HIS N 168 PHE 0.030 0.002 PHE 7 54 TYR 0.021 0.001 TYR R 72 ARG 0.005 0.000 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 244 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: 1 60 MET cc_start: 0.7479 (tpp) cc_final: 0.7078 (tpp) REVERT: 1 63 PHE cc_start: 0.7695 (t80) cc_final: 0.7467 (t80) REVERT: 2 72 LEU cc_start: 0.8336 (tp) cc_final: 0.8029 (tp) REVERT: 3 51 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5865 (tp) REVERT: 3 66 MET cc_start: 0.6684 (ttp) cc_final: 0.5368 (tpt) REVERT: 5 39 ASN cc_start: 0.8681 (p0) cc_final: 0.8299 (p0) REVERT: 6 47 PHE cc_start: 0.8333 (t80) cc_final: 0.7890 (t80) REVERT: 7 51 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7911 (tp) REVERT: 7 71 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8160 (tt) REVERT: 8 62 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (tt) REVERT: K 28 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8118 (mttp) REVERT: K 87 GLU cc_start: 0.8697 (tt0) cc_final: 0.8447 (mt-10) REVERT: K 114 GLN cc_start: 0.6843 (mt0) cc_final: 0.6478 (mm-40) REVERT: M 107 GLN cc_start: 0.7698 (pt0) cc_final: 0.7138 (pm20) REVERT: M 111 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: M 138 GLU cc_start: 0.8870 (tt0) cc_final: 0.8499 (tm-30) REVERT: M 152 TYR cc_start: 0.8937 (m-80) cc_final: 0.8628 (m-80) REVERT: N 46 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6731 (mp10) REVERT: N 149 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8626 (tp) REVERT: Q 4 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8562 (mt) REVERT: R 8 LYS cc_start: 0.8534 (mptt) cc_final: 0.8282 (mmtm) REVERT: R 14 GLU cc_start: 0.8124 (tp30) cc_final: 0.7781 (tp30) REVERT: R 46 TYR cc_start: 0.8508 (t80) cc_final: 0.8213 (t80) outliers start: 60 outliers final: 44 residues processed: 279 average time/residue: 0.2096 time to fit residues: 85.8931 Evaluate side-chains 290 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 34 ILE Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 8 residue 62 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 13 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11273 Z= 0.308 Angle : 0.681 8.563 15116 Z= 0.340 Chirality : 0.041 0.182 1712 Planarity : 0.005 0.069 1807 Dihedral : 14.400 118.668 1994 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.46 % Allowed : 24.54 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1340 helix: 0.56 (0.16), residues: 1049 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 25 HIS 0.004 0.001 HIS N 168 PHE 0.034 0.002 PHE 7 54 TYR 0.023 0.002 TYR R 72 ARG 0.005 0.000 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 1.273 Fit side-chains REVERT: 1 60 MET cc_start: 0.7406 (tpp) cc_final: 0.6982 (tpp) REVERT: 1 63 PHE cc_start: 0.7684 (t80) cc_final: 0.7433 (t80) REVERT: 2 46 LEU cc_start: 0.7021 (mp) cc_final: 0.6714 (mt) REVERT: 2 72 LEU cc_start: 0.8361 (tp) cc_final: 0.8050 (tp) REVERT: 4 49 TYR cc_start: 0.7939 (m-80) cc_final: 0.7526 (t80) REVERT: 6 47 PHE cc_start: 0.8305 (t80) cc_final: 0.7870 (t80) REVERT: 7 71 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8175 (tt) REVERT: 8 62 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8096 (tt) REVERT: K 87 GLU cc_start: 0.8709 (tt0) cc_final: 0.8458 (mt-10) REVERT: K 114 GLN cc_start: 0.6963 (mt0) cc_final: 0.6559 (mm-40) REVERT: M 107 GLN cc_start: 0.7883 (pt0) cc_final: 0.7591 (pt0) REVERT: M 138 GLU cc_start: 0.8921 (tt0) cc_final: 0.8556 (tm-30) REVERT: M 152 TYR cc_start: 0.9026 (m-80) cc_final: 0.8643 (m-80) REVERT: N 46 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: N 131 GLN cc_start: 0.8741 (pm20) cc_final: 0.8146 (tt0) REVERT: N 149 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8727 (tp) REVERT: Q 4 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8629 (mt) REVERT: R 8 LYS cc_start: 0.8598 (mptt) cc_final: 0.8355 (mmtm) REVERT: R 14 GLU cc_start: 0.8151 (tp30) cc_final: 0.7768 (tp30) REVERT: R 46 TYR cc_start: 0.8595 (t80) cc_final: 0.8363 (t80) REVERT: S 93 ILE cc_start: 0.8665 (tp) cc_final: 0.8428 (tt) outliers start: 59 outliers final: 44 residues processed: 284 average time/residue: 0.2084 time to fit residues: 85.9364 Evaluate side-chains 287 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 238 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 67 VAL Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 8 residue 62 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 82 optimal weight: 0.0870 chunk 110 optimal weight: 10.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11273 Z= 0.227 Angle : 0.642 8.565 15116 Z= 0.319 Chirality : 0.039 0.183 1712 Planarity : 0.005 0.071 1807 Dihedral : 14.118 116.773 1994 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.72 % Allowed : 25.46 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1340 helix: 0.63 (0.16), residues: 1049 sheet: None (None), residues: 0 loop : -1.56 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 25 HIS 0.003 0.001 HIS N 168 PHE 0.042 0.002 PHE 6 54 TYR 0.023 0.001 TYR 3 49 ARG 0.011 0.001 ARG M 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: 1 63 PHE cc_start: 0.7677 (t80) cc_final: 0.7436 (t80) REVERT: 2 72 LEU cc_start: 0.8368 (tp) cc_final: 0.8045 (tp) REVERT: 6 47 PHE cc_start: 0.8273 (t80) cc_final: 0.7914 (t80) REVERT: 7 51 ILE cc_start: 0.8125 (tp) cc_final: 0.7753 (tt) REVERT: 8 62 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8083 (tt) REVERT: K 19 GLU cc_start: 0.8827 (tp30) cc_final: 0.8531 (tp30) REVERT: K 28 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8060 (mttp) REVERT: K 87 GLU cc_start: 0.8691 (tt0) cc_final: 0.8441 (mt-10) REVERT: K 114 GLN cc_start: 0.6920 (mt0) cc_final: 0.6561 (mm-40) REVERT: M 138 GLU cc_start: 0.8899 (tt0) cc_final: 0.8471 (tm-30) REVERT: N 46 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.6726 (mp10) REVERT: N 131 GLN cc_start: 0.8643 (pm20) cc_final: 0.8095 (tt0) REVERT: N 149 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8608 (tp) REVERT: Q 4 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8556 (mt) REVERT: R 14 GLU cc_start: 0.8058 (tp30) cc_final: 0.7677 (tp30) REVERT: R 46 TYR cc_start: 0.8508 (t80) cc_final: 0.8222 (t80) REVERT: S 93 ILE cc_start: 0.8626 (tp) cc_final: 0.8371 (tt) outliers start: 51 outliers final: 40 residues processed: 275 average time/residue: 0.2058 time to fit residues: 82.4309 Evaluate side-chains 282 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 62 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 86 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117189 restraints weight = 16909.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120247 restraints weight = 8717.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122250 restraints weight = 5456.412| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11273 Z= 0.244 Angle : 0.679 10.293 15116 Z= 0.335 Chirality : 0.040 0.183 1712 Planarity : 0.005 0.074 1807 Dihedral : 14.005 115.764 1994 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.72 % Allowed : 25.93 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1340 helix: 0.62 (0.16), residues: 1055 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 25 HIS 0.003 0.001 HIS N 168 PHE 0.041 0.002 PHE 6 54 TYR 0.025 0.002 TYR 3 49 ARG 0.010 0.001 ARG M 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.97 seconds wall clock time: 41 minutes 9.34 seconds (2469.34 seconds total)