Starting phenix.real_space_refine on Fri Feb 16 10:41:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/02_2024/6ucv_20729_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/02_2024/6ucv_20729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/02_2024/6ucv_20729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/02_2024/6ucv_20729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/02_2024/6ucv_20729_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/02_2024/6ucv_20729_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 2 5.49 5 S 44 5.16 5 C 9682 2.51 5 N 2523 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "I ARG 52": "NH1" <-> "NH2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 219": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "I ARG 330": "NH1" <-> "NH2" Residue "J ARG 89": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 219": "NH1" <-> "NH2" Residue "a ARG 235": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "i ARG 52": "NH1" <-> "NH2" Residue "i PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 219": "NH1" <-> "NH2" Residue "i ARG 235": "NH1" <-> "NH2" Residue "i ARG 330": "NH1" <-> "NH2" Residue "j ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15102 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2399 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 267 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2419 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "b" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 397 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 267 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "e" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "i" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "j" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "k" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "m" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'MC3': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'MC3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.67, per 1000 atoms: 0.51 Number of scatterers: 15102 At special positions: 0 Unit cell: (100.05, 120.75, 215.05, 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 44 16.00 P 2 15.00 O 2851 8.00 N 2523 7.00 C 9682 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: 5.13 Conformation dependent library (CDL) restraints added in 2.6 seconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 34.5% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.638A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 134 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 48 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'E' and resid 12 through 30 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.652A pdb=" N LEU E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 54' Processing helix chain 'I' and resid 46 through 55 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 365 through 372 removed outlier: 3.689A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 134 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 48 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 31 through 50 Processing helix chain 'L' and resid 52 through 57 Processing helix chain 'M' and resid 12 through 30 Processing helix chain 'M' and resid 32 through 42 Processing helix chain 'M' and resid 50 through 54 removed outlier: 3.504A pdb=" N LEU M 54 " --> pdb=" O PHE M 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 50 through 54' Processing helix chain 'a' and resid 40 through 53 Processing helix chain 'a' and resid 68 through 71 No H-bonds generated for 'chain 'a' and resid 68 through 71' Processing helix chain 'a' and resid 365 through 372 removed outlier: 3.754A pdb=" N GLN a 372 " --> pdb=" O LEU a 368 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 134 Proline residue: b 112 - end of helix Processing helix chain 'c' and resid 14 through 48 Proline residue: c 39 - end of helix Processing helix chain 'd' and resid 30 through 50 removed outlier: 4.031A pdb=" N THR d 34 " --> pdb=" O SER d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 57 Processing helix chain 'e' and resid 12 through 30 Processing helix chain 'e' and resid 32 through 42 Processing helix chain 'e' and resid 50 through 54 removed outlier: 3.692A pdb=" N LEU e 54 " --> pdb=" O PHE e 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 50 through 54' Processing helix chain 'i' and resid 50 through 54 Processing helix chain 'i' and resid 68 through 71 No H-bonds generated for 'chain 'i' and resid 68 through 71' Processing helix chain 'i' and resid 365 through 372 removed outlier: 3.581A pdb=" N GLN i 372 " --> pdb=" O LEU i 368 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 134 Proline residue: j 112 - end of helix Processing helix chain 'k' and resid 14 through 48 Proline residue: k 39 - end of helix Processing helix chain 'l' and resid 31 through 50 Processing helix chain 'l' and resid 52 through 57 Processing helix chain 'm' and resid 12 through 30 Processing helix chain 'm' and resid 32 through 42 Processing helix chain 'm' and resid 50 through 54 removed outlier: 3.512A pdb=" N LEU m 54 " --> pdb=" O PHE m 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 50 through 54' Processing sheet with id= A, first strand: chain 'A' and resid 85 through 91 removed outlier: 4.232A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 93 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR A 100 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA A 91 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS A 102 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN A 89 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE A 104 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 87 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 106 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG A 85 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 83 through 91 removed outlier: 4.286A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER I 93 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR I 100 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ALA I 91 " --> pdb=" O THR I 100 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N HIS I 102 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASN I 89 " --> pdb=" O HIS I 102 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE I 104 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP I 87 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE I 106 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG I 85 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 85 through 91 removed outlier: 4.306A pdb=" N LYS a 323 " --> pdb=" O ASP a 319 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER a 93 " --> pdb=" O PHE a 98 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR a 100 " --> pdb=" O ALA a 91 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA a 91 " --> pdb=" O THR a 100 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N HIS a 102 " --> pdb=" O ASN a 89 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN a 89 " --> pdb=" O HIS a 102 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE a 104 " --> pdb=" O ASP a 87 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP a 87 " --> pdb=" O PHE a 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'i' and resid 83 through 91 removed outlier: 4.204A pdb=" N LYS i 323 " --> pdb=" O ASP i 319 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER i 93 " --> pdb=" O PHE i 98 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR i 100 " --> pdb=" O ALA i 91 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA i 91 " --> pdb=" O THR i 100 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS i 102 " --> pdb=" O ASN i 89 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN i 89 " --> pdb=" O HIS i 102 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE i 104 " --> pdb=" O ASP i 87 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP i 87 " --> pdb=" O PHE i 104 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE i 106 " --> pdb=" O ARG i 85 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ARG i 85 " --> pdb=" O ILE i 106 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2994 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: 5.30 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2487 1.30 - 1.43: 4065 1.43 - 1.56: 8770 1.56 - 1.69: 24 1.69 - 1.81: 72 Bond restraints: 15418 Sorted by residual: bond pdb=" C31 MC3 I 401 " pdb=" O2 MC3 I 401 " ideal model delta sigma weight residual 1.328 1.433 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C31 MC3 i 401 " pdb=" O2 MC3 i 401 " ideal model delta sigma weight residual 1.328 1.432 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C11 MC3 i 401 " pdb=" O3 MC3 i 401 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C11 MC3 I 401 " pdb=" O3 MC3 I 401 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" N MC3 i 401 " pdb=" C8 MC3 i 401 " ideal model delta sigma weight residual 1.493 1.429 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 15413 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.06: 416 107.06 - 113.80: 8641 113.80 - 120.53: 5925 120.53 - 127.27: 5776 127.27 - 134.00: 157 Bond angle restraints: 20915 Sorted by residual: angle pdb=" O1P MC3 i 401 " pdb=" P MC3 i 401 " pdb=" O2P MC3 i 401 " ideal model delta sigma weight residual 119.69 100.88 18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" O1P MC3 I 401 " pdb=" P MC3 I 401 " pdb=" O2P MC3 I 401 " ideal model delta sigma weight residual 119.69 101.69 18.00 3.00e+00 1.11e-01 3.60e+01 angle pdb=" O3P MC3 I 401 " pdb=" P MC3 I 401 " pdb=" O4P MC3 I 401 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O3P MC3 i 401 " pdb=" P MC3 i 401 " pdb=" O4P MC3 i 401 " ideal model delta sigma weight residual 93.26 109.81 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" CA ASP a 134 " pdb=" CB ASP a 134 " pdb=" CG ASP a 134 " ideal model delta sigma weight residual 112.60 117.22 -4.62 1.00e+00 1.00e+00 2.13e+01 ... (remaining 20910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.82: 8797 19.82 - 39.64: 259 39.64 - 59.46: 58 59.46 - 79.27: 2 79.27 - 99.09: 1 Dihedral angle restraints: 9117 sinusoidal: 3494 harmonic: 5623 Sorted by residual: dihedral pdb=" CA ASN i 95 " pdb=" C ASN i 95 " pdb=" N PRO i 96 " pdb=" CA PRO i 96 " ideal model delta harmonic sigma weight residual 180.00 139.35 40.65 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA ASN a 95 " pdb=" C ASN a 95 " pdb=" N PRO a 96 " pdb=" CA PRO a 96 " ideal model delta harmonic sigma weight residual 180.00 139.79 40.21 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 140.83 39.17 0 5.00e+00 4.00e-02 6.14e+01 ... (remaining 9114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2100 0.078 - 0.156: 256 0.156 - 0.234: 18 0.234 - 0.312: 2 0.312 - 0.390: 4 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CB ILE m 33 " pdb=" CA ILE m 33 " pdb=" CG1 ILE m 33 " pdb=" CG2 ILE m 33 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE M 33 " pdb=" CA ILE M 33 " pdb=" CG1 ILE M 33 " pdb=" CG2 ILE M 33 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB ILE e 33 " pdb=" CA ILE e 33 " pdb=" CG1 ILE e 33 " pdb=" CG2 ILE e 33 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2377 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO A 207 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR a 206 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO a 207 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO a 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 207 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 206 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO I 207 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " 0.036 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1412 2.75 - 3.29: 13790 3.29 - 3.82: 24164 3.82 - 4.36: 26785 4.36 - 4.90: 48949 Nonbonded interactions: 115100 Sorted by model distance: nonbonded pdb=" OD1 ASN a 179 " pdb=" OG SER a 200 " model vdw 2.210 2.440 nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASN i 179 " pdb=" OG SER i 200 " model vdw 2.261 2.440 nonbonded pdb=" OG SER A 312 " pdb=" OG SER B 116 " model vdw 2.279 2.440 ... (remaining 115095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 49 through 373) selection = (chain 'I' and resid 49 through 373) selection = (chain 'a' and resid 49 through 373) selection = (chain 'i' and resid 49 through 373) } ncs_group { reference = chain 'B' selection = (chain 'J' and resid 86 through 135) selection = (chain 'b' and resid 86 through 135) selection = chain 'j' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'D' and ((resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 61)) selection = (chain 'L' and resid 27 through 61) selection = (chain 'd' and resid 27 through 61) selection = (chain 'l' and ((resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 61)) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'e' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.020 Extract box with map and model: 13.930 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 39.760 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 15418 Z= 0.340 Angle : 0.941 18.813 20915 Z= 0.481 Chirality : 0.053 0.390 2380 Planarity : 0.007 0.067 2661 Dihedral : 10.415 99.092 5473 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.87 (0.17), residues: 1899 helix: -1.31 (0.14), residues: 724 sheet: -0.34 (0.18), residues: 808 loop : -2.50 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 100 HIS 0.005 0.001 HIS C 43 PHE 0.025 0.002 PHE b 92 TYR 0.015 0.002 TYR E 30 ARG 0.006 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9115 (tp) cc_final: 0.8831 (tp) REVERT: A 170 ASP cc_start: 0.8507 (t0) cc_final: 0.8262 (m-30) REVERT: A 171 TYR cc_start: 0.8367 (t80) cc_final: 0.8137 (t80) REVERT: I 369 MET cc_start: 0.8764 (mtp) cc_final: 0.8481 (tmm) REVERT: K 40 MET cc_start: 0.7006 (mpm) cc_final: 0.6411 (mpp) REVERT: M 54 LEU cc_start: 0.8884 (mp) cc_final: 0.8591 (tt) REVERT: a 303 ILE cc_start: 0.9077 (tt) cc_final: 0.8798 (mp) REVERT: e 38 TYR cc_start: 0.7540 (t80) cc_final: 0.6442 (m-80) REVERT: m 53 LEU cc_start: 0.8775 (tt) cc_final: 0.8465 (mt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2197 time to fit residues: 71.3049 Evaluate side-chains 84 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 17 HIS D 50 GLN E 29 HIS I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN K 17 HIS M 29 HIS a 99 GLN ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 17 HIS e 52 ASN i 99 GLN k 17 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15418 Z= 0.260 Angle : 0.617 7.859 20915 Z= 0.320 Chirality : 0.040 0.153 2380 Planarity : 0.005 0.053 2661 Dihedral : 7.400 101.532 2109 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 0.04 (0.19), residues: 1899 helix: 1.19 (0.18), residues: 724 sheet: -0.17 (0.18), residues: 818 loop : -1.57 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 36 HIS 0.006 0.001 HIS A 102 PHE 0.023 0.001 PHE C 34 TYR 0.013 0.002 TYR E 30 ARG 0.004 0.000 ARG a 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8007 (tpt) cc_final: 0.7670 (tmm) REVERT: C 40 MET cc_start: 0.8317 (mpp) cc_final: 0.7909 (mpp) REVERT: I 211 LEU cc_start: 0.9289 (mt) cc_final: 0.8697 (tt) REVERT: M 54 LEU cc_start: 0.9118 (mp) cc_final: 0.8690 (tt) REVERT: i 271 ILE cc_start: 0.9282 (tt) cc_final: 0.9068 (mt) REVERT: m 53 LEU cc_start: 0.8784 (tt) cc_final: 0.8448 (mt) outliers start: 2 outliers final: 2 residues processed: 99 average time/residue: 0.2032 time to fit residues: 34.1475 Evaluate side-chains 66 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 40.0000 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 0.0030 chunk 170 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN a 99 GLN d 38 ASN e 29 HIS e 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15418 Z= 0.331 Angle : 0.671 8.067 20915 Z= 0.349 Chirality : 0.041 0.160 2380 Planarity : 0.004 0.053 2661 Dihedral : 7.310 66.588 2109 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.67 (0.20), residues: 1899 helix: 2.07 (0.19), residues: 717 sheet: -0.17 (0.18), residues: 815 loop : -1.16 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 36 HIS 0.008 0.001 HIS A 102 PHE 0.022 0.002 PHE A 359 TYR 0.022 0.002 TYR E 30 ARG 0.005 0.001 ARG a 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 VAL cc_start: 0.9244 (t) cc_final: 0.8936 (t) REVERT: C 40 MET cc_start: 0.8615 (mpp) cc_final: 0.7964 (mpp) REVERT: I 369 MET cc_start: 0.8555 (tmm) cc_final: 0.8305 (tmm) REVERT: M 54 LEU cc_start: 0.9275 (mp) cc_final: 0.8837 (tt) REVERT: c 40 MET cc_start: 0.8832 (mpp) cc_final: 0.8589 (mpp) REVERT: m 53 LEU cc_start: 0.8804 (tt) cc_final: 0.8438 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2072 time to fit residues: 27.5261 Evaluate side-chains 58 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 0.0030 chunk 81 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN M 52 ASN a 99 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15418 Z= 0.189 Angle : 0.580 7.902 20915 Z= 0.295 Chirality : 0.039 0.144 2380 Planarity : 0.004 0.050 2661 Dihedral : 6.706 64.279 2109 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1899 helix: 2.52 (0.19), residues: 721 sheet: -0.08 (0.18), residues: 817 loop : -0.70 (0.37), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 36 HIS 0.004 0.001 HIS A 51 PHE 0.014 0.001 PHE i 359 TYR 0.012 0.001 TYR I 307 ARG 0.003 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7868 (tpt) cc_final: 0.7634 (tpp) REVERT: C 37 VAL cc_start: 0.9153 (t) cc_final: 0.8908 (p) REVERT: C 40 MET cc_start: 0.8541 (mpp) cc_final: 0.7918 (mpp) REVERT: D 54 MET cc_start: 0.8272 (tpp) cc_final: 0.7779 (tpp) REVERT: I 369 MET cc_start: 0.8530 (tmm) cc_final: 0.8240 (tmm) REVERT: L 54 MET cc_start: 0.8632 (tpt) cc_final: 0.8372 (tpp) REVERT: M 54 LEU cc_start: 0.9252 (mp) cc_final: 0.8811 (tt) REVERT: c 40 MET cc_start: 0.8896 (mpp) cc_final: 0.8567 (mpp) REVERT: m 53 LEU cc_start: 0.8809 (tt) cc_final: 0.8429 (mt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2084 time to fit residues: 30.8685 Evaluate side-chains 61 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN I 172 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN J 90 ASN M 52 ASN a 99 GLN e 52 ASN m 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15418 Z= 0.431 Angle : 0.726 8.852 20915 Z= 0.380 Chirality : 0.043 0.152 2380 Planarity : 0.004 0.053 2661 Dihedral : 7.360 67.428 2109 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.92 (0.20), residues: 1899 helix: 2.38 (0.19), residues: 718 sheet: -0.19 (0.18), residues: 805 loop : -0.85 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 145 HIS 0.009 0.002 HIS A 102 PHE 0.023 0.002 PHE i 359 TYR 0.026 0.002 TYR E 30 ARG 0.006 0.001 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9082 (tp) cc_final: 0.8649 (tt) REVERT: A 369 MET cc_start: 0.8184 (tpt) cc_final: 0.7947 (tpp) REVERT: C 37 VAL cc_start: 0.9168 (t) cc_final: 0.8933 (t) REVERT: C 40 MET cc_start: 0.8570 (mpp) cc_final: 0.8078 (mpp) REVERT: I 79 TYR cc_start: 0.8814 (m-80) cc_final: 0.8594 (m-80) REVERT: L 54 MET cc_start: 0.8805 (tpt) cc_final: 0.8602 (tpp) REVERT: M 54 LEU cc_start: 0.9172 (mp) cc_final: 0.8825 (tt) outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.2077 time to fit residues: 25.4828 Evaluate side-chains 54 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN M 52 ASN a 99 GLN e 52 ASN i 166 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15418 Z= 0.285 Angle : 0.636 8.160 20915 Z= 0.331 Chirality : 0.041 0.149 2380 Planarity : 0.004 0.049 2661 Dihedral : 6.992 68.230 2109 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1899 helix: 2.52 (0.19), residues: 718 sheet: -0.17 (0.18), residues: 804 loop : -0.73 (0.36), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 41 HIS 0.009 0.001 HIS i 51 PHE 0.016 0.001 PHE i 359 TYR 0.015 0.001 TYR I 307 ARG 0.003 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8170 (tpt) cc_final: 0.7929 (tpp) REVERT: C 37 VAL cc_start: 0.9255 (t) cc_final: 0.8980 (t) REVERT: C 40 MET cc_start: 0.8543 (mpp) cc_final: 0.8074 (mpp) REVERT: D 54 MET cc_start: 0.8314 (tpp) cc_final: 0.7988 (tpp) REVERT: I 369 MET cc_start: 0.8542 (tmm) cc_final: 0.8161 (tmm) REVERT: M 54 LEU cc_start: 0.9145 (mp) cc_final: 0.8800 (tt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1962 time to fit residues: 24.8700 Evaluate side-chains 56 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN I 133 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** K 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15418 Z= 0.239 Angle : 0.621 8.132 20915 Z= 0.318 Chirality : 0.040 0.145 2380 Planarity : 0.004 0.049 2661 Dihedral : 6.806 68.008 2109 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.06 % Allowed : 1.75 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.15 (0.21), residues: 1899 helix: 2.65 (0.19), residues: 718 sheet: -0.18 (0.18), residues: 810 loop : -0.64 (0.37), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 41 HIS 0.006 0.001 HIS A 102 PHE 0.013 0.001 PHE I 359 TYR 0.017 0.001 TYR I 307 ARG 0.003 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9009 (tp) cc_final: 0.8541 (tt) REVERT: A 369 MET cc_start: 0.8174 (tpt) cc_final: 0.7942 (tpp) REVERT: C 37 VAL cc_start: 0.9246 (t) cc_final: 0.8985 (t) REVERT: C 40 MET cc_start: 0.8535 (mpp) cc_final: 0.8087 (mpp) REVERT: D 54 MET cc_start: 0.8237 (tpp) cc_final: 0.7895 (tpp) REVERT: I 369 MET cc_start: 0.8521 (tmm) cc_final: 0.8149 (tmm) REVERT: M 54 LEU cc_start: 0.9086 (mp) cc_final: 0.8792 (tt) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.2171 time to fit residues: 27.7871 Evaluate side-chains 56 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN J 90 ASN M 52 ASN a 99 GLN a 133 ASN e 29 HIS e 52 ASN i 99 GLN i 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15418 Z= 0.161 Angle : 0.593 7.964 20915 Z= 0.301 Chirality : 0.040 0.180 2380 Planarity : 0.004 0.050 2661 Dihedral : 6.453 65.302 2109 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 0.06 % Allowed : 1.31 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % 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: 1.43 (0.21), residues: 1899 helix: 2.87 (0.19), residues: 719 sheet: -0.06 (0.18), residues: 805 loop : -0.44 (0.38), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 41 HIS 0.004 0.001 HIS A 51 PHE 0.013 0.001 PHE I 359 TYR 0.013 0.001 TYR I 307 ARG 0.003 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8960 (tp) cc_final: 0.8738 (tp) REVERT: A 369 MET cc_start: 0.8149 (tpt) cc_final: 0.7923 (tpp) REVERT: C 37 VAL cc_start: 0.9240 (t) cc_final: 0.9025 (p) REVERT: C 40 MET cc_start: 0.8484 (mpp) cc_final: 0.8038 (mpp) REVERT: D 54 MET cc_start: 0.8339 (tpp) cc_final: 0.7987 (tpp) REVERT: I 369 MET cc_start: 0.8448 (tmm) cc_final: 0.8086 (tmm) REVERT: M 54 LEU cc_start: 0.9172 (mp) cc_final: 0.8860 (tt) REVERT: j 102 LEU cc_start: 0.8956 (tp) cc_final: 0.8629 (tt) REVERT: l 54 MET cc_start: 0.9244 (tpp) cc_final: 0.9041 (tpp) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.2053 time to fit residues: 28.0672 Evaluate side-chains 59 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 110 optimal weight: 0.0570 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN M 52 ASN a 99 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15418 Z= 0.210 Angle : 0.607 8.020 20915 Z= 0.308 Chirality : 0.040 0.181 2380 Planarity : 0.004 0.048 2661 Dihedral : 6.545 64.492 2109 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % 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: 1.44 (0.21), residues: 1899 helix: 2.86 (0.19), residues: 721 sheet: -0.04 (0.18), residues: 801 loop : -0.41 (0.38), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 41 HIS 0.005 0.001 HIS A 102 PHE 0.014 0.001 PHE i 359 TYR 0.010 0.001 TYR e 38 ARG 0.003 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9004 (tp) cc_final: 0.8516 (tt) REVERT: A 369 MET cc_start: 0.8147 (tpt) cc_final: 0.7911 (tpp) REVERT: C 37 VAL cc_start: 0.9222 (t) cc_final: 0.9018 (p) REVERT: C 40 MET cc_start: 0.8507 (mpp) cc_final: 0.8111 (mpp) REVERT: D 54 MET cc_start: 0.8311 (tpp) cc_final: 0.7913 (tpp) REVERT: I 369 MET cc_start: 0.8439 (tmm) cc_final: 0.8080 (tmm) REVERT: L 54 MET cc_start: 0.8630 (tpt) cc_final: 0.8425 (tpp) REVERT: M 54 LEU cc_start: 0.9171 (mp) cc_final: 0.8901 (tt) REVERT: l 54 MET cc_start: 0.9255 (tpp) cc_final: 0.9046 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2382 time to fit residues: 30.7652 Evaluate side-chains 59 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN I 133 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN J 90 ASN K 43 HIS M 52 ASN a 99 GLN e 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15418 Z= 0.271 Angle : 0.639 8.104 20915 Z= 0.328 Chirality : 0.041 0.169 2380 Planarity : 0.004 0.048 2661 Dihedral : 6.767 65.501 2109 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.32 (0.21), residues: 1899 helix: 2.78 (0.19), residues: 718 sheet: -0.10 (0.18), residues: 806 loop : -0.52 (0.38), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP m 41 HIS 0.007 0.001 HIS i 51 PHE 0.026 0.001 PHE b 92 TYR 0.012 0.001 TYR e 38 ARG 0.003 0.000 ARG I 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9046 (tp) cc_final: 0.8559 (tt) REVERT: A 369 MET cc_start: 0.8254 (tpt) cc_final: 0.8017 (tpp) REVERT: C 37 VAL cc_start: 0.9257 (t) cc_final: 0.8990 (t) REVERT: C 40 MET cc_start: 0.8560 (mpp) cc_final: 0.8090 (mpp) REVERT: D 54 MET cc_start: 0.8341 (tpp) cc_final: 0.7939 (tpp) REVERT: I 369 MET cc_start: 0.8455 (tmm) cc_final: 0.8096 (tmm) REVERT: L 54 MET cc_start: 0.8765 (tpt) cc_final: 0.8538 (tpp) REVERT: M 54 LEU cc_start: 0.9165 (mp) cc_final: 0.8959 (tt) REVERT: l 54 MET cc_start: 0.9245 (tpp) cc_final: 0.9038 (tpp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2078 time to fit residues: 26.0459 Evaluate side-chains 56 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN e 52 ASN i 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.048331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038987 restraints weight = 115637.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039225 restraints weight = 70644.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039367 restraints weight = 63547.927| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15418 Z= 0.467 Angle : 0.772 9.758 20915 Z= 0.401 Chirality : 0.044 0.180 2380 Planarity : 0.004 0.047 2661 Dihedral : 7.497 70.542 2109 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.71 (0.20), residues: 1899 helix: 2.30 (0.19), residues: 717 sheet: -0.39 (0.18), residues: 803 loop : -0.91 (0.36), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP m 41 HIS 0.022 0.002 HIS i 51 PHE 0.031 0.002 PHE b 92 TYR 0.026 0.002 TYR I 307 ARG 0.005 0.001 ARG I 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.58 seconds wall clock time: 42 minutes 33.57 seconds (2553.57 seconds total)