Starting phenix.real_space_refine (version: dev) on Sun May 15 02:15:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/05_2022/7mqd_23943.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/05_2022/7mqd_23943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/05_2022/7mqd_23943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/05_2022/7mqd_23943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/05_2022/7mqd_23943.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/05_2022/7mqd_23943.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ASP 164": "OD1" <-> "OD2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M ASP 164": "OD1" <-> "OD2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M ASP 193": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O ASP 164": "OD1" <-> "OD2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O ASP 193": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 11960 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "I" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "K" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "M" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "O" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 101 Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.58 Number of scatterers: 11960 At special positions: 0 Unit cell: (105.4, 105.4, 85.56, 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 48 16.00 P 16 15.00 O 2088 8.00 N 2176 7.00 C 7632 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: 4.76 Conformation dependent library (CDL) restraints added in 2.1 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 46.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 155 removed outlier: 3.501A pdb=" N ASP O 155 " --> pdb=" O TYR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.181A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.181A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.180A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.180A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.181A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.181A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.181A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA M 23 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8 removed outlier: 6.181A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3841 1.34 - 1.45: 1632 1.45 - 1.57: 6655 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12216 Sorted by residual: bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.08e-02 8.57e+03 4.43e-01 bond pdb=" N VAL M 156 " pdb=" CA VAL M 156 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.08e-02 8.57e+03 4.28e-01 bond pdb=" CB VAL I 40 " pdb=" CG1 VAL I 40 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.13e-01 bond pdb=" CB VAL C 40 " pdb=" CG1 VAL C 40 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" C ARG M 161 " pdb=" O ARG M 161 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 3.94e-01 ... (remaining 12211 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.23: 481 107.23 - 113.93: 7055 113.93 - 120.63: 4916 120.63 - 127.33: 4092 127.33 - 134.03: 168 Bond angle restraints: 16712 Sorted by residual: angle pdb=" CA GLN A 42 " pdb=" CB GLN A 42 " pdb=" CG GLN A 42 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.01e+00 angle pdb=" CA GLN C 42 " pdb=" CB GLN C 42 " pdb=" CG GLN C 42 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.99e+00 angle pdb=" CA GLN M 42 " pdb=" CB GLN M 42 " pdb=" CG GLN M 42 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CA GLN I 42 " pdb=" CB GLN I 42 " pdb=" CG GLN I 42 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.89e+00 angle pdb=" CA GLN O 42 " pdb=" CB GLN O 42 " pdb=" CG GLN O 42 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.88e+00 ... (remaining 16707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6714 17.83 - 35.66: 310 35.66 - 53.49: 64 53.49 - 71.32: 32 71.32 - 89.15: 16 Dihedral angle restraints: 7136 sinusoidal: 2504 harmonic: 4632 Sorted by residual: dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE C 78 " pdb=" C PHE C 78 " pdb=" N HIS C 79 " pdb=" CA HIS C 79 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE G 78 " pdb=" C PHE G 78 " pdb=" N HIS G 79 " pdb=" CA HIS G 79 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1071 0.028 - 0.056: 526 0.056 - 0.083: 256 0.083 - 0.111: 131 0.111 - 0.139: 64 Chirality restraints: 2048 Sorted by residual: chirality pdb=" CA ILE G 4 " pdb=" N ILE G 4 " pdb=" C ILE G 4 " pdb=" CB ILE G 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE M 4 " pdb=" N ILE M 4 " pdb=" C ILE M 4 " pdb=" CB ILE M 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE I 4 " pdb=" N ILE I 4 " pdb=" C ILE I 4 " pdb=" CB ILE I 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 2045 not shown) Planarity restraints: 2048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 83 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.76e+00 pdb=" C PHE G 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE G 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 84 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 83 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C PHE E 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE E 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP E 84 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 83 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C PHE O 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE O 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP O 84 " -0.008 2.00e-02 2.50e+03 ... (remaining 2045 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 5116 2.94 - 3.43: 11286 3.43 - 3.92: 19745 3.92 - 4.41: 23107 4.41 - 4.90: 37981 Nonbonded interactions: 97235 Sorted by model distance: nonbonded pdb=" O HIS G 205 " pdb=" NZ LYS O 103 " model vdw 2.456 2.520 nonbonded pdb=" NZ LYS E 103 " pdb=" O HIS I 205 " model vdw 2.490 2.520 nonbonded pdb=" OG1 THR G 26 " pdb=" OD1 ASP G 84 " model vdw 2.499 2.440 nonbonded pdb=" OG1 THR C 26 " pdb=" OD1 ASP C 84 " model vdw 2.499 2.440 nonbonded pdb=" OG1 THR I 26 " pdb=" OD1 ASP I 84 " model vdw 2.499 2.440 ... (remaining 97230 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 48 5.16 5 C 7632 2.51 5 N 2176 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.000 Extract box with map and model: 1.730 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 33.640 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.003 0.021 12216 Z= 0.209 Angle : 0.617 5.660 16712 Z= 0.372 Chirality : 0.046 0.139 2048 Planarity : 0.004 0.026 2048 Dihedral : 13.347 89.151 4112 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1560 helix: 0.79 (0.19), residues: 704 sheet: 0.50 (0.22), residues: 240 loop : 0.94 (0.28), residues: 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2427 time to fit residues: 48.8732 Evaluate side-chains 137 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.040 12216 Z= 0.441 Angle : 0.576 4.639 16712 Z= 0.301 Chirality : 0.048 0.133 2048 Planarity : 0.005 0.033 2048 Dihedral : 6.548 53.216 1872 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1560 helix: 1.54 (0.20), residues: 704 sheet: 0.83 (0.27), residues: 240 loop : 0.79 (0.29), residues: 616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.289 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 0.2277 time to fit residues: 41.6088 Evaluate side-chains 126 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0973 time to fit residues: 2.4279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12216 Z= 0.298 Angle : 0.482 4.495 16712 Z= 0.255 Chirality : 0.045 0.126 2048 Planarity : 0.004 0.032 2048 Dihedral : 6.369 53.538 1872 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1560 helix: 1.46 (0.20), residues: 704 sheet: 1.41 (0.29), residues: 240 loop : 0.56 (0.28), residues: 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.397 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 119 average time/residue: 0.2055 time to fit residues: 37.5142 Evaluate side-chains 119 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 12216 Z= 0.303 Angle : 0.478 4.485 16712 Z= 0.252 Chirality : 0.045 0.125 2048 Planarity : 0.004 0.032 2048 Dihedral : 6.423 55.311 1872 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1560 helix: 1.29 (0.20), residues: 704 sheet: 1.46 (0.29), residues: 240 loop : 0.44 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.233 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 116 average time/residue: 0.1974 time to fit residues: 35.8183 Evaluate side-chains 116 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 12216 Z= 0.235 Angle : 0.437 4.462 16712 Z= 0.233 Chirality : 0.043 0.123 2048 Planarity : 0.003 0.031 2048 Dihedral : 6.330 56.176 1872 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1560 helix: 1.39 (0.20), residues: 704 sheet: 1.64 (0.29), residues: 240 loop : 0.52 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.442 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 114 average time/residue: 0.1817 time to fit residues: 33.3897 Evaluate side-chains 114 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 12216 Z= 0.126 Angle : 0.379 4.438 16712 Z= 0.207 Chirality : 0.042 0.119 2048 Planarity : 0.003 0.028 2048 Dihedral : 6.015 55.705 1872 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.22), residues: 1560 helix: 1.69 (0.20), residues: 704 sheet: 1.95 (0.30), residues: 240 loop : 0.64 (0.28), residues: 616 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.315 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 129 average time/residue: 0.1739 time to fit residues: 36.3650 Evaluate side-chains 109 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1422 time to fit residues: 2.0547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 0.0270 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 overall best weight: 2.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 12216 Z= 0.287 Angle : 0.459 4.542 16712 Z= 0.243 Chirality : 0.044 0.124 2048 Planarity : 0.003 0.031 2048 Dihedral : 6.303 56.031 1872 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.22), residues: 1560 helix: 1.42 (0.20), residues: 704 sheet: 1.93 (0.29), residues: 240 loop : 0.53 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.473 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 121 average time/residue: 0.1818 time to fit residues: 35.3410 Evaluate side-chains 116 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1470 time to fit residues: 2.0532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 12216 Z= 0.405 Angle : 0.514 4.620 16712 Z= 0.270 Chirality : 0.046 0.128 2048 Planarity : 0.004 0.032 2048 Dihedral : 6.573 55.754 1872 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1560 helix: 1.14 (0.19), residues: 704 sheet: 1.70 (0.29), residues: 240 loop : 0.39 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.473 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 0.1809 time to fit residues: 34.4070 Evaluate side-chains 116 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1148 time to fit residues: 2.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 12216 Z= 0.230 Angle : 0.428 4.481 16712 Z= 0.230 Chirality : 0.043 0.123 2048 Planarity : 0.003 0.030 2048 Dihedral : 6.400 56.685 1872 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1560 helix: 1.32 (0.20), residues: 704 sheet: 1.84 (0.29), residues: 240 loop : 0.46 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.326 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.1755 time to fit residues: 31.6621 Evaluate side-chains 110 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1017 time to fit residues: 1.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 12216 Z= 0.118 Angle : 0.371 4.416 16712 Z= 0.203 Chirality : 0.042 0.119 2048 Planarity : 0.003 0.029 2048 Dihedral : 5.994 55.659 1872 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1560 helix: 1.62 (0.20), residues: 704 sheet: 2.11 (0.30), residues: 240 loop : 0.56 (0.27), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.432 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1842 time to fit residues: 31.0662 Evaluate side-chains 101 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.120786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102272 restraints weight = 13692.013| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.39 r_work: 0.3055 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 1.27 restraints_weight: 0.2500 r_work: 0.3016 rms_B_bonded: 1.44 restraints_weight: 0.1250 r_work: 0.2991 rms_B_bonded: 1.72 restraints_weight: 0.0625 r_work: 0.2959 rms_B_bonded: 2.12 restraints_weight: 0.0312 r_work: 0.2918 rms_B_bonded: 2.67 restraints_weight: 0.0156 r_work: 0.2866 rms_B_bonded: 3.45 restraints_weight: 0.0078 r_work: 0.2795 rms_B_bonded: 4.56 restraints_weight: 0.0039 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 12216 Z= 0.193 Angle : 0.402 4.425 16712 Z= 0.217 Chirality : 0.043 0.120 2048 Planarity : 0.003 0.030 2048 Dihedral : 6.113 55.753 1872 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1560 helix: 1.54 (0.20), residues: 704 sheet: 2.09 (0.30), residues: 240 loop : 0.48 (0.27), residues: 616 =============================================================================== Job complete usr+sys time: 1624.20 seconds wall clock time: 30 minutes 49.59 seconds (1849.59 seconds total)