Starting phenix.real_space_refine on Thu Dec 14 19:48:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/12_2023/7bok_30131_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/12_2023/7bok_30131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/12_2023/7bok_30131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/12_2023/7bok_30131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/12_2023/7bok_30131_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/12_2023/7bok_30131_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Fe 12 7.16 5 S 108 5.16 5 C 18480 2.51 5 N 4848 2.21 5 O 5664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 267": "NH1" <-> "NH2" Residue "J PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 119": "OE1" <-> "OE2" Residue "K TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 267": "NH1" <-> "NH2" Residue "K PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 267": "NH1" <-> "NH2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29112 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "D" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "E" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "F" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "H" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "J" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "K" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "L" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.81, per 1000 atoms: 0.51 Number of scatterers: 29112 At special positions: 0 Unit cell: (184.08, 115.44, 108.16, 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) Fe 12 26.01 S 108 16.00 O 5664 8.00 N 4848 7.00 C 18480 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.55 Conformation dependent library (CDL) restraints added in 5.1 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 24 sheets defined 28.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 Proline residue: A 37 - end of helix removed outlier: 5.309A pdb=" N SER A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL A 159 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 190' Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'B' and resid 29 through 46 Proline residue: B 37 - end of helix removed outlier: 5.309A pdb=" N SER B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL B 159 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 190' Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'C' and resid 29 through 46 Proline residue: C 37 - end of helix removed outlier: 5.309A pdb=" N SER C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 190' Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'D' and resid 29 through 46 Proline residue: D 37 - end of helix removed outlier: 5.309A pdb=" N SER D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL D 159 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.590A pdb=" N SER D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 190' Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'E' and resid 29 through 46 Proline residue: E 37 - end of helix removed outlier: 5.310A pdb=" N SER E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL E 159 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 190' Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'F' and resid 29 through 46 Proline residue: F 37 - end of helix removed outlier: 5.310A pdb=" N SER F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 63 through 69 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL F 159 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 170 No H-bonds generated for 'chain 'F' and resid 168 through 170' Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 186 through 190' Processing helix chain 'F' and resid 193 through 200 Processing helix chain 'F' and resid 220 through 224 Processing helix chain 'F' and resid 262 through 272 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'G' and resid 29 through 46 Proline residue: G 37 - end of helix removed outlier: 5.309A pdb=" N SER G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY G 41 " --> pdb=" O PRO G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL G 159 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 186 through 190' Processing helix chain 'G' and resid 193 through 200 Processing helix chain 'G' and resid 220 through 223 No H-bonds generated for 'chain 'G' and resid 220 through 223' Processing helix chain 'G' and resid 262 through 272 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'H' and resid 29 through 46 Proline residue: H 37 - end of helix removed outlier: 5.309A pdb=" N SER H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY H 41 " --> pdb=" O PRO H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 53 No H-bonds generated for 'chain 'H' and resid 51 through 53' Processing helix chain 'H' and resid 63 through 69 Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL H 159 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 186 through 190' Processing helix chain 'H' and resid 193 through 200 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'H' and resid 262 through 272 Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'I' and resid 29 through 46 Proline residue: I 37 - end of helix removed outlier: 5.309A pdb=" N SER I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY I 41 " --> pdb=" O PRO I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 63 through 69 Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL I 159 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 190' Processing helix chain 'I' and resid 193 through 200 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 262 through 272 Processing helix chain 'I' and resid 301 through 305 Processing helix chain 'J' and resid 29 through 46 Proline residue: J 37 - end of helix removed outlier: 5.309A pdb=" N SER J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 63 through 69 Processing helix chain 'J' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU J 119 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL J 159 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 170 No H-bonds generated for 'chain 'J' and resid 168 through 170' Processing helix chain 'J' and resid 186 through 190 removed outlier: 3.590A pdb=" N SER J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 186 through 190' Processing helix chain 'J' and resid 193 through 200 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 262 through 272 Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'K' and resid 29 through 46 Proline residue: K 37 - end of helix removed outlier: 5.310A pdb=" N SER K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY K 41 " --> pdb=" O PRO K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 53 No H-bonds generated for 'chain 'K' and resid 51 through 53' Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU K 119 " --> pdb=" O THR K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL K 159 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 186 through 190' Processing helix chain 'K' and resid 193 through 200 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 262 through 272 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'L' and resid 29 through 46 Proline residue: L 37 - end of helix removed outlier: 5.310A pdb=" N SER L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY L 41 " --> pdb=" O PRO L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU L 119 " --> pdb=" O THR L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL L 159 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 186 through 190' Processing helix chain 'L' and resid 193 through 200 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 301 through 305 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR A 131 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR A 23 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE A 127 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 294 through 298 Processing sheet with id= C, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR B 131 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 23 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE B 127 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= E, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR C 131 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 23 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE C 127 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 294 through 298 Processing sheet with id= G, first strand: chain 'D' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR D 131 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 23 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE D 127 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= I, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR E 131 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR E 23 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE E 127 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 294 through 298 Processing sheet with id= K, first strand: chain 'F' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR F 131 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR F 23 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE F 127 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 294 through 298 Processing sheet with id= M, first strand: chain 'G' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR G 131 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR G 23 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE G 127 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 294 through 298 Processing sheet with id= O, first strand: chain 'H' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR H 131 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR H 23 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE H 127 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 294 through 298 Processing sheet with id= Q, first strand: chain 'I' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR I 131 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR I 23 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE I 127 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 294 through 298 Processing sheet with id= S, first strand: chain 'J' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR J 131 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR J 23 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE J 127 " --> pdb=" O THR J 23 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 294 through 298 Processing sheet with id= U, first strand: chain 'K' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR K 131 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR K 23 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE K 127 " --> pdb=" O THR K 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 294 through 298 Processing sheet with id= W, first strand: chain 'L' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR L 131 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR L 23 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE L 127 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 294 through 298 898 hydrogen bonds defined for protein. 2298 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: 9.81 Time building geometry restraints manager: 12.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 12468 1.40 - 1.57: 17208 1.57 - 1.75: 0 1.75 - 1.93: 204 1.93 - 2.10: 36 Bond restraints: 29916 Sorted by residual: bond pdb=" C3B HEM J 401 " pdb=" CAB HEM J 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM D 401 " pdb=" CAB HEM D 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM A 401 " pdb=" CAB HEM A 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM G 401 " pdb=" CAB HEM G 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM E 401 " pdb=" CAB HEM E 401 " ideal model delta sigma weight residual 1.544 1.469 0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 29911 not shown) Histogram of bond angle deviations from ideal: 86.22 - 104.40: 862 104.40 - 122.58: 35632 122.58 - 140.76: 4426 140.76 - 158.94: 0 158.94 - 177.12: 24 Bond angle restraints: 40944 Sorted by residual: angle pdb=" N VAL C 193 " pdb=" CA VAL C 193 " pdb=" C VAL C 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" N VAL I 193 " pdb=" CA VAL I 193 " pdb=" C VAL I 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" N VAL D 193 " pdb=" CA VAL D 193 " pdb=" C VAL D 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.62e+01 angle pdb=" N VAL J 193 " pdb=" CA VAL J 193 " pdb=" C VAL J 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.62e+01 angle pdb=" N VAL E 193 " pdb=" CA VAL E 193 " pdb=" C VAL E 193 " ideal model delta sigma weight residual 110.62 117.07 -6.45 1.02e+00 9.61e-01 4.00e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15906 17.22 - 34.43: 1254 34.43 - 51.65: 314 51.65 - 68.86: 22 68.86 - 86.08: 72 Dihedral angle restraints: 17568 sinusoidal: 7032 harmonic: 10536 Sorted by residual: dihedral pdb=" C2B HEM A 401 " pdb=" C3B HEM A 401 " pdb=" CAB HEM A 401 " pdb=" CBB HEM A 401 " ideal model delta sinusoidal sigma weight residual 180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C2B HEM G 401 " pdb=" C3B HEM G 401 " pdb=" CAB HEM G 401 " pdb=" CBB HEM G 401 " ideal model delta sinusoidal sigma weight residual -180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C2B HEM E 401 " pdb=" C3B HEM E 401 " pdb=" CAB HEM E 401 " pdb=" CBB HEM E 401 " ideal model delta sinusoidal sigma weight residual -180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3242 0.055 - 0.110: 1018 0.110 - 0.165: 118 0.165 - 0.220: 0 0.220 - 0.275: 14 Chirality restraints: 4392 Sorted by residual: chirality pdb=" CA VAL G 225 " pdb=" N VAL G 225 " pdb=" C VAL G 225 " pdb=" CB VAL G 225 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE B 256 " pdb=" CA ILE B 256 " pdb=" CG1 ILE B 256 " pdb=" CG2 ILE B 256 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4389 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEM G 401 " -0.034 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" CGD HEM G 401 " 0.114 2.00e-02 2.50e+03 pdb=" O1D HEM G 401 " -0.041 2.00e-02 2.50e+03 pdb=" O2D HEM G 401 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM A 401 " 0.034 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" CGD HEM A 401 " -0.114 2.00e-02 2.50e+03 pdb=" O1D HEM A 401 " 0.041 2.00e-02 2.50e+03 pdb=" O2D HEM A 401 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM J 401 " -0.033 2.00e-02 2.50e+03 6.61e-02 4.36e+01 pdb=" CGD HEM J 401 " 0.114 2.00e-02 2.50e+03 pdb=" O1D HEM J 401 " -0.041 2.00e-02 2.50e+03 pdb=" O2D HEM J 401 " -0.040 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 353 2.61 - 3.18: 24499 3.18 - 3.75: 48114 3.75 - 4.33: 67871 4.33 - 4.90: 108629 Nonbonded interactions: 249466 Sorted by model distance: nonbonded pdb=" NH1 ARG F 198 " pdb=" CA SER I 187 " model vdw 2.036 3.550 nonbonded pdb=" CA SER C 187 " pdb=" NH1 ARG L 198 " model vdw 2.036 3.550 nonbonded pdb=" OG1 THR C 149 " pdb=" O ARG E 44 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR I 149 " pdb=" O ARG K 44 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR G 149 " pdb=" O ARG I 44 " model vdw 2.257 2.440 ... (remaining 249461 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.880 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 75.030 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.009 0.223 29916 Z= 0.581 Angle : 0.923 7.121 40944 Z= 0.496 Chirality : 0.051 0.275 4392 Planarity : 0.009 0.066 5484 Dihedral : 14.399 86.079 10800 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % 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: -3.42 (0.13), residues: 3684 helix: -3.40 (0.12), residues: 996 sheet: -2.20 (0.19), residues: 876 loop : -1.46 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 66 HIS 0.004 0.001 HIS G 79 PHE 0.010 0.002 PHE C 303 TYR 0.009 0.002 TYR E 255 ARG 0.002 0.000 ARG I 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.4523 time to fit residues: 451.2853 Evaluate side-chains 258 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 239 HIS B 271 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS H 239 HIS H 271 ASN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 HIS ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29916 Z= 0.345 Angle : 0.664 6.858 40944 Z= 0.325 Chirality : 0.042 0.187 4392 Planarity : 0.006 0.045 5484 Dihedral : 10.082 89.867 4056 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.17 % Allowed : 15.21 % Favored : 82.62 % 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: -2.38 (0.13), residues: 3684 helix: -2.13 (0.13), residues: 1068 sheet: -1.85 (0.19), residues: 828 loop : -0.88 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 66 HIS 0.008 0.001 HIS F 183 PHE 0.011 0.001 PHE D 303 TYR 0.015 0.002 TYR K 181 ARG 0.006 0.001 ARG I 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 310 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 37 residues processed: 357 average time/residue: 0.4048 time to fit residues: 233.6299 Evaluate side-chains 275 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2776 time to fit residues: 23.3489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 0.3980 chunk 272 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 0.0570 chunk 353 optimal weight: 0.8980 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS B 132 HIS B 177 HIS B 240 ASN B 271 ASN C 183 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 183 HIS ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS H 132 HIS H 177 HIS H 240 ASN H 271 ASN I 183 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN L 183 HIS ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29916 Z= 0.243 Angle : 0.601 6.529 40944 Z= 0.289 Chirality : 0.040 0.133 4392 Planarity : 0.005 0.050 5484 Dihedral : 9.664 86.772 4056 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.10 % Allowed : 15.73 % Favored : 83.17 % 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: -1.72 (0.14), residues: 3684 helix: -1.23 (0.14), residues: 1080 sheet: -1.64 (0.18), residues: 828 loop : -0.63 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 66 HIS 0.010 0.001 HIS L 183 PHE 0.010 0.001 PHE C 251 TYR 0.022 0.001 TYR K 181 ARG 0.005 0.000 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 289 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 10 residues processed: 317 average time/residue: 0.3882 time to fit residues: 201.0471 Evaluate side-chains 253 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 243 time to evaluate : 3.293 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2590 time to fit residues: 9.2254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 29916 Z= 0.411 Angle : 0.670 9.402 40944 Z= 0.326 Chirality : 0.042 0.189 4392 Planarity : 0.005 0.055 5484 Dihedral : 9.307 88.784 4056 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.30 % Allowed : 16.37 % Favored : 81.32 % 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: -1.23 (0.14), residues: 3684 helix: -0.59 (0.15), residues: 1080 sheet: -1.29 (0.19), residues: 828 loop : -0.55 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 66 HIS 0.006 0.001 HIS G 239 PHE 0.014 0.002 PHE G 296 TYR 0.023 0.002 TYR K 181 ARG 0.004 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 262 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 38 residues processed: 317 average time/residue: 0.4026 time to fit residues: 207.6951 Evaluate side-chains 259 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 3.561 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2734 time to fit residues: 23.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 271 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS H 271 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29916 Z= 0.303 Angle : 0.601 6.418 40944 Z= 0.290 Chirality : 0.041 0.146 4392 Planarity : 0.005 0.041 5484 Dihedral : 9.049 86.257 4056 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.59 % Allowed : 17.57 % Favored : 80.84 % 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: -0.90 (0.14), residues: 3684 helix: -0.18 (0.16), residues: 1080 sheet: -1.09 (0.19), residues: 828 loop : -0.45 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 66 HIS 0.004 0.001 HIS J 177 PHE 0.014 0.001 PHE B 251 TYR 0.020 0.001 TYR K 181 ARG 0.006 0.000 ARG K 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 294 average time/residue: 0.3870 time to fit residues: 189.1069 Evaluate side-chains 235 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 3.670 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2695 time to fit residues: 14.2114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.0970 chunk 313 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 0.0970 chunk 85 optimal weight: 5.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 overall best weight: 0.9778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS A 224 ASN B 224 ASN B 271 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS G 224 ASN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29916 Z= 0.238 Angle : 0.577 6.644 40944 Z= 0.275 Chirality : 0.040 0.141 4392 Planarity : 0.004 0.038 5484 Dihedral : 8.836 84.474 4056 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.26 % Allowed : 18.55 % Favored : 80.19 % 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: -0.61 (0.14), residues: 3684 helix: 0.11 (0.16), residues: 1092 sheet: -0.89 (0.19), residues: 828 loop : -0.33 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 66 HIS 0.007 0.001 HIS E 183 PHE 0.019 0.001 PHE I 251 TYR 0.026 0.001 TYR B 255 ARG 0.004 0.000 ARG K 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 286 average time/residue: 0.3720 time to fit residues: 177.3436 Evaluate side-chains 236 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2848 time to fit residues: 12.8398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 9.9990 chunk 39 optimal weight: 0.0170 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 29916 Z= 0.401 Angle : 0.650 7.746 40944 Z= 0.314 Chirality : 0.042 0.199 4392 Planarity : 0.005 0.045 5484 Dihedral : 8.816 84.732 4056 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.56 % Allowed : 18.55 % Favored : 79.90 % 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: -0.63 (0.14), residues: 3684 helix: 0.06 (0.16), residues: 1092 sheet: -0.81 (0.19), residues: 828 loop : -0.37 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 66 HIS 0.006 0.001 HIS F 220 PHE 0.017 0.002 PHE C 251 TYR 0.036 0.002 TYR B 255 ARG 0.004 0.000 ARG K 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 258 average time/residue: 0.3885 time to fit residues: 166.2902 Evaluate side-chains 229 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 3.548 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2785 time to fit residues: 19.2348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 271 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS H 224 ASN H 271 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29916 Z= 0.242 Angle : 0.596 12.848 40944 Z= 0.283 Chirality : 0.040 0.153 4392 Planarity : 0.004 0.039 5484 Dihedral : 8.696 84.558 4056 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.45 % Allowed : 19.03 % Favored : 80.51 % 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: -0.43 (0.14), residues: 3684 helix: 0.33 (0.16), residues: 1092 sheet: -0.71 (0.19), residues: 828 loop : -0.31 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 188 HIS 0.006 0.001 HIS H 183 PHE 0.015 0.001 PHE I 251 TYR 0.037 0.002 TYR H 255 ARG 0.003 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 251 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 261 average time/residue: 0.4174 time to fit residues: 183.9027 Evaluate side-chains 229 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 3.279 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2586 time to fit residues: 6.2502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 29916 Z= 0.456 Angle : 0.702 11.311 40944 Z= 0.336 Chirality : 0.043 0.172 4392 Planarity : 0.005 0.054 5484 Dihedral : 8.812 87.122 4056 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.75 % Allowed : 19.52 % Favored : 79.73 % 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: -0.61 (0.14), residues: 3684 helix: 0.14 (0.16), residues: 1068 sheet: -0.66 (0.19), residues: 828 loop : -0.48 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 66 HIS 0.007 0.001 HIS H 183 PHE 0.016 0.002 PHE I 137 TYR 0.029 0.002 TYR K 181 ARG 0.004 0.001 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 236 average time/residue: 0.4188 time to fit residues: 163.7380 Evaluate side-chains 202 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 3.281 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3014 time to fit residues: 11.7279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 9.9990 chunk 341 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 358 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN C 132 HIS ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN I 132 HIS ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 29916 Z= 0.336 Angle : 0.643 12.253 40944 Z= 0.306 Chirality : 0.042 0.141 4392 Planarity : 0.005 0.040 5484 Dihedral : 8.742 87.371 4056 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.29 % Allowed : 20.10 % Favored : 79.60 % 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: -0.54 (0.14), residues: 3684 helix: 0.27 (0.16), residues: 1068 sheet: -0.65 (0.19), residues: 828 loop : -0.47 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 66 HIS 0.007 0.001 HIS B 183 PHE 0.021 0.001 PHE I 251 TYR 0.027 0.002 TYR B 255 ARG 0.003 0.000 ARG K 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 223 average time/residue: 0.3834 time to fit residues: 142.8583 Evaluate side-chains 203 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 3.382 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2574 time to fit residues: 5.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 286 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 chunk 293 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 ASN ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.073855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065549 restraints weight = 95704.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067409 restraints weight = 48498.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068677 restraints weight = 29897.032| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 29916 Z= 0.269 Angle : 0.614 11.954 40944 Z= 0.290 Chirality : 0.041 0.129 4392 Planarity : 0.004 0.036 5484 Dihedral : 8.612 86.506 4056 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.36 % Allowed : 20.46 % Favored : 79.18 % 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: -0.37 (0.14), residues: 3684 helix: 0.43 (0.17), residues: 1068 sheet: -0.52 (0.19), residues: 816 loop : -0.40 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.006 0.001 HIS H 183 PHE 0.020 0.001 PHE I 251 TYR 0.019 0.001 TYR K 181 ARG 0.003 0.000 ARG E 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5007.41 seconds wall clock time: 92 minutes 59.21 seconds (5579.21 seconds total)