Starting phenix.real_space_refine on Sat Sep 28 18:12:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/09_2024/6bqw_7134.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/09_2024/6bqw_7134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/09_2024/6bqw_7134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/09_2024/6bqw_7134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/09_2024/6bqw_7134.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bqw_7134/09_2024/6bqw_7134.cif" } resolution = 4.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 27 5.49 5 S 135 5.16 5 C 12681 2.51 5 N 3168 2.21 5 O 3942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19953 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H Time building chain proxies: 6.64, per 1000 atoms: 0.33 Number of scatterers: 19953 At special positions: 0 Unit cell: (100, 100, 270, 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 135 16.00 P 27 15.00 O 3942 8.00 N 3168 7.00 C 12681 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 - 3.00 Amino acid : True - 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: 4.72 Conformation dependent library (CDL) restraints added in 2.2 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 54 sheets defined 36.0% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL C 260 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 275 removed outlier: 3.573A pdb=" N ALA C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL D 260 " --> pdb=" O TYR D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 200 through 212 Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL E 260 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE F 86 " --> pdb=" O MET F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 114 through 127 Processing helix chain 'F' and resid 152 through 158 Processing helix chain 'F' and resid 200 through 212 Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 3.903A pdb=" N VAL F 260 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE G 86 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 114 through 127 Processing helix chain 'G' and resid 152 through 158 Processing helix chain 'G' and resid 200 through 212 Processing helix chain 'G' and resid 227 through 239 Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 3.905A pdb=" N VAL G 260 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 Processing helix chain 'H' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE H 86 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 114 through 127 Processing helix chain 'H' and resid 152 through 158 Processing helix chain 'H' and resid 200 through 212 Processing helix chain 'H' and resid 227 through 239 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL H 260 " --> pdb=" O TYR H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 Processing helix chain 'I' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE I 86 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 114 through 127 Processing helix chain 'I' and resid 152 through 158 Processing helix chain 'I' and resid 200 through 212 Processing helix chain 'I' and resid 227 through 239 Processing helix chain 'I' and resid 253 through 255 No H-bonds generated for 'chain 'I' and resid 253 through 255' Processing helix chain 'I' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL I 260 " --> pdb=" O TYR I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 275 removed outlier: 3.573A pdb=" N ALA I 275 " --> pdb=" O GLU I 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL A 6 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 5 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 109 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 7 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA6, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 224 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL A 167 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL B 6 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 5 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 109 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE B 7 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB3, first strand: chain 'B' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL B 165 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 224 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 167 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL C 6 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR C 5 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR C 109 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 7 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 131 Processing sheet with id=AB8, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AB9, first strand: chain 'C' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL C 165 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR C 224 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL C 167 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'D' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL D 6 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 5 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR D 109 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 7 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 33 through 35 Processing sheet with id=AC4, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AC5, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AC6, first strand: chain 'D' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL D 165 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 224 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 167 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 25 through 26 removed outlier: 4.632A pdb=" N VAL E 6 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR E 5 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR E 109 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE E 7 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AD1, first strand: chain 'E' and resid 128 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AD3, first strand: chain 'E' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL E 165 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 224 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 167 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD5, first strand: chain 'F' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL F 6 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR F 5 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR F 109 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE F 7 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AD7, first strand: chain 'F' and resid 128 through 131 Processing sheet with id=AD8, first strand: chain 'F' and resid 183 through 184 Processing sheet with id=AD9, first strand: chain 'F' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL F 165 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR F 224 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL F 167 " --> pdb=" O THR F 224 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'G' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL G 6 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR G 5 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR G 109 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE G 7 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AE4, first strand: chain 'G' and resid 128 through 131 Processing sheet with id=AE5, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AE6, first strand: chain 'G' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL G 165 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR G 224 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL G 167 " --> pdb=" O THR G 224 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AE8, first strand: chain 'H' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL H 6 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR H 5 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR H 109 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE H 7 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 33 through 35 Processing sheet with id=AF1, first strand: chain 'H' and resid 128 through 131 Processing sheet with id=AF2, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AF3, first strand: chain 'H' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL H 165 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR H 224 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL H 167 " --> pdb=" O THR H 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AF5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL I 6 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR I 5 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR I 109 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE I 7 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 33 through 35 Processing sheet with id=AF7, first strand: chain 'I' and resid 128 through 131 Processing sheet with id=AF8, first strand: chain 'I' and resid 183 through 184 Processing sheet with id=AF9, first strand: chain 'I' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL I 165 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR I 224 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL I 167 " --> pdb=" O THR I 224 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2322 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: 6.66 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5496 1.33 - 1.45: 4579 1.45 - 1.57: 10049 1.57 - 1.69: 18 1.69 - 1.82: 225 Bond restraints: 20367 Sorted by residual: bond pdb=" N3B ANP G 301 " pdb=" PG ANP G 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3B ANP C 301 " pdb=" PG ANP C 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N3B ANP H 301 " pdb=" PG ANP H 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 ... (remaining 20362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 24313 1.81 - 3.61: 2610 3.61 - 5.42: 428 5.42 - 7.22: 57 7.22 - 9.03: 78 Bond angle restraints: 27486 Sorted by residual: angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 119.93 128.43 -8.50 1.07e+00 8.73e-01 6.31e+01 angle pdb=" C LYS E 252 " pdb=" N PRO E 253 " pdb=" CA PRO E 253 " ideal model delta sigma weight residual 119.93 128.43 -8.50 1.07e+00 8.73e-01 6.30e+01 angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 119.93 128.42 -8.49 1.07e+00 8.73e-01 6.30e+01 angle pdb=" C LYS I 252 " pdb=" N PRO I 253 " pdb=" CA PRO I 253 " ideal model delta sigma weight residual 119.93 128.41 -8.48 1.07e+00 8.73e-01 6.28e+01 angle pdb=" C LYS H 252 " pdb=" N PRO H 253 " pdb=" CA PRO H 253 " ideal model delta sigma weight residual 119.93 128.40 -8.47 1.07e+00 8.73e-01 6.27e+01 ... (remaining 27481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 12024 35.79 - 71.58: 153 71.58 - 107.37: 18 107.37 - 143.16: 0 143.16 - 178.95: 9 Dihedral angle restraints: 12204 sinusoidal: 5040 harmonic: 7164 Sorted by residual: dihedral pdb=" CA CYS H 164 " pdb=" C CYS H 164 " pdb=" N VAL H 165 " pdb=" CA VAL H 165 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS E 164 " pdb=" C CYS E 164 " pdb=" N VAL E 165 " pdb=" CA VAL E 165 " ideal model delta harmonic sigma weight residual 180.00 -155.76 -24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS D 164 " pdb=" C CYS D 164 " pdb=" N VAL D 165 " pdb=" CA VAL D 165 " ideal model delta harmonic sigma weight residual 180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1739 0.061 - 0.123: 1002 0.123 - 0.184: 198 0.184 - 0.245: 22 0.245 - 0.307: 9 Chirality restraints: 2970 Sorted by residual: chirality pdb=" C2' ANP E 301 " pdb=" C1' ANP E 301 " pdb=" C3' ANP E 301 " pdb=" O2' ANP E 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ANP D 301 " pdb=" C1' ANP D 301 " pdb=" C3' ANP D 301 " pdb=" O2' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ANP H 301 " pdb=" C1' ANP H 301 " pdb=" C3' ANP H 301 " pdb=" O2' ANP H 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2967 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 164 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C CYS A 164 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS A 164 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 165 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 164 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C CYS C 164 " 0.043 2.00e-02 2.50e+03 pdb=" O CYS C 164 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 165 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 164 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C CYS D 164 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS D 164 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL D 165 " 0.014 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7458 2.83 - 3.34: 21057 3.34 - 3.86: 36382 3.86 - 4.38: 44731 4.38 - 4.90: 67976 Nonbonded interactions: 177604 Sorted by model distance: nonbonded pdb=" OG SER H 171 " pdb=" N LYS H 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER F 171 " pdb=" N LYS F 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER G 171 " pdb=" N LYS G 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER A 171 " pdb=" N LYS A 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER D 171 " pdb=" N LYS D 172 " model vdw 2.307 3.120 ... (remaining 177599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.020 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.016 0.168 20367 Z= 1.039 Angle : 1.278 9.026 27486 Z= 0.807 Chirality : 0.073 0.307 2970 Planarity : 0.006 0.025 3447 Dihedral : 13.915 178.952 7686 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 5.86 % Allowed : 10.26 % Favored : 83.88 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -3.51 (0.14), residues: 2457 helix: -1.08 (0.16), residues: 747 sheet: -2.61 (0.17), residues: 432 loop : -3.07 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 34 PHE 0.010 0.003 PHE A 64 TYR 0.032 0.006 TYR G 56 ARG 0.003 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7448 (mmm) cc_final: 0.7098 (tpp) REVERT: B 48 VAL cc_start: 0.8139 (t) cc_final: 0.7654 (p) REVERT: B 88 LEU cc_start: 0.8119 (tp) cc_final: 0.7901 (tp) REVERT: B 95 ILE cc_start: 0.8275 (pt) cc_final: 0.7868 (pt) REVERT: C 187 MET cc_start: 0.5628 (ptt) cc_final: 0.5051 (ptp) REVERT: C 201 ILE cc_start: 0.8640 (mt) cc_final: 0.8402 (tp) REVERT: C 211 THR cc_start: 0.8373 (p) cc_final: 0.7331 (p) REVERT: C 235 LEU cc_start: 0.8170 (mt) cc_final: 0.7657 (mm) REVERT: C 259 SER cc_start: 0.8407 (p) cc_final: 0.8192 (t) REVERT: D 5 THR cc_start: 0.7657 (p) cc_final: 0.7448 (p) REVERT: D 32 ILE cc_start: 0.9133 (mt) cc_final: 0.7760 (mt) REVERT: D 180 ILE cc_start: 0.8687 (mt) cc_final: 0.8419 (pt) REVERT: D 202 MET cc_start: 0.7947 (mmm) cc_final: 0.7689 (tpp) REVERT: E 99 THR cc_start: 0.8488 (p) cc_final: 0.8173 (p) REVERT: E 159 SER cc_start: 0.8344 (m) cc_final: 0.8069 (p) REVERT: E 184 ILE cc_start: 0.8996 (mt) cc_final: 0.8779 (mt) REVERT: F 95 ILE cc_start: 0.8715 (pt) cc_final: 0.8268 (pt) REVERT: F 108 LEU cc_start: 0.8473 (mt) cc_final: 0.8118 (mt) REVERT: F 115 MET cc_start: 0.7695 (mtp) cc_final: 0.7295 (mtm) REVERT: F 159 SER cc_start: 0.8623 (m) cc_final: 0.8316 (p) REVERT: F 187 MET cc_start: 0.6185 (ptt) cc_final: 0.5639 (ptt) REVERT: F 259 SER cc_start: 0.8797 (p) cc_final: 0.8548 (p) REVERT: G 5 THR cc_start: 0.7288 (p) cc_final: 0.7022 (p) REVERT: G 95 ILE cc_start: 0.8708 (pt) cc_final: 0.8331 (pt) REVERT: H 88 LEU cc_start: 0.7980 (tp) cc_final: 0.7693 (tp) REVERT: H 222 VAL cc_start: 0.7908 (t) cc_final: 0.7694 (t) REVERT: H 235 LEU cc_start: 0.8311 (mt) cc_final: 0.7361 (mt) REVERT: I 211 THR cc_start: 0.8198 (p) cc_final: 0.7536 (p) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.3848 time to fit residues: 361.0937 Evaluate side-chains 368 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS A 163 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 144 HIS ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 HIS ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20367 Z= 0.278 Angle : 0.799 8.838 27486 Z= 0.433 Chirality : 0.049 0.191 2970 Planarity : 0.004 0.032 3447 Dihedral : 13.221 179.595 2997 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 2.52 % Allowed : 11.27 % Favored : 86.20 % Rotamer: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.36 (0.16), residues: 2457 helix: -0.22 (0.18), residues: 747 sheet: -2.50 (0.17), residues: 603 loop : -1.85 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 125 PHE 0.028 0.002 PHE E 158 TYR 0.024 0.002 TYR E 256 ARG 0.004 0.001 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 465 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7615 (mmm) cc_final: 0.7298 (tpp) REVERT: A 211 THR cc_start: 0.8190 (p) cc_final: 0.7759 (p) REVERT: B 141 PHE cc_start: 0.5537 (p90) cc_final: 0.5124 (p90) REVERT: C 15 LYS cc_start: 0.7103 (ptpp) cc_final: 0.6837 (ptpp) REVERT: C 63 ASN cc_start: 0.7865 (m110) cc_final: 0.7549 (t0) REVERT: C 187 MET cc_start: 0.5556 (ptt) cc_final: 0.5135 (ptp) REVERT: C 259 SER cc_start: 0.8500 (p) cc_final: 0.8141 (t) REVERT: D 87 ARG cc_start: 0.8381 (mtt-85) cc_final: 0.8076 (mtm-85) REVERT: E 45 MET cc_start: 0.6824 (mtt) cc_final: 0.6618 (mtt) REVERT: E 92 LEU cc_start: 0.9383 (mt) cc_final: 0.9117 (mt) REVERT: E 108 LEU cc_start: 0.8361 (mt) cc_final: 0.8076 (mt) REVERT: E 148 MET cc_start: 0.6936 (mmm) cc_final: 0.6310 (mmm) REVERT: E 157 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.7548 (p0) REVERT: E 202 MET cc_start: 0.7827 (mmm) cc_final: 0.7367 (mmm) REVERT: E 211 THR cc_start: 0.8405 (p) cc_final: 0.7895 (p) REVERT: F 95 ILE cc_start: 0.8684 (pt) cc_final: 0.8269 (mm) REVERT: F 98 GLU cc_start: 0.7065 (pt0) cc_final: 0.6760 (pt0) REVERT: F 106 LEU cc_start: 0.7240 (tp) cc_final: 0.6951 (tp) REVERT: F 202 MET cc_start: 0.8103 (mmm) cc_final: 0.7778 (tpp) REVERT: F 259 SER cc_start: 0.8803 (p) cc_final: 0.8533 (t) REVERT: G 1 MET cc_start: 0.6497 (mtm) cc_final: 0.5535 (mpp) REVERT: G 6 VAL cc_start: 0.8076 (t) cc_final: 0.7804 (t) REVERT: G 77 THR cc_start: 0.6749 (p) cc_final: 0.6537 (p) outliers start: 3 outliers final: 1 residues processed: 467 average time/residue: 0.3580 time to fit residues: 243.6793 Evaluate side-chains 310 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS B 63 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS C 63 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 105 ASN D 144 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS F 163 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS I 34 HIS ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20367 Z= 0.405 Angle : 0.828 8.641 27486 Z= 0.443 Chirality : 0.050 0.200 2970 Planarity : 0.005 0.044 3447 Dihedral : 12.839 178.430 2997 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 2.24 % Allowed : 12.74 % Favored : 85.02 % Rotamer: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.47 (0.16), residues: 2457 helix: -0.44 (0.17), residues: 756 sheet: -2.19 (0.19), residues: 585 loop : -2.10 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 125 PHE 0.020 0.002 PHE H 122 TYR 0.027 0.003 TYR H 217 ARG 0.010 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 374 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7411 (ptpp) cc_final: 0.7115 (ptpp) REVERT: C 63 ASN cc_start: 0.8026 (m-40) cc_final: 0.7823 (t0) REVERT: C 73 TYR cc_start: 0.7293 (m-80) cc_final: 0.7028 (m-80) REVERT: C 187 MET cc_start: 0.5384 (ptt) cc_final: 0.4499 (ptp) REVERT: C 259 SER cc_start: 0.8576 (p) cc_final: 0.8162 (t) REVERT: E 94 THR cc_start: 0.8528 (p) cc_final: 0.8143 (t) REVERT: E 115 MET cc_start: 0.8006 (tpp) cc_final: 0.7522 (tpp) REVERT: E 148 MET cc_start: 0.7256 (mmm) cc_final: 0.6747 (mtm) REVERT: E 262 LEU cc_start: 0.8585 (tp) cc_final: 0.8375 (tp) REVERT: F 1 MET cc_start: 0.7451 (mtm) cc_final: 0.7199 (mtm) REVERT: F 73 TYR cc_start: 0.7430 (m-80) cc_final: 0.7224 (m-80) REVERT: F 106 LEU cc_start: 0.7523 (tp) cc_final: 0.7295 (tp) REVERT: F 259 SER cc_start: 0.8763 (p) cc_final: 0.8563 (t) REVERT: G 108 LEU cc_start: 0.7944 (mt) cc_final: 0.7678 (mt) outliers start: 3 outliers final: 0 residues processed: 376 average time/residue: 0.3679 time to fit residues: 203.1504 Evaluate side-chains 257 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN D 163 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 144 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN H 144 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN I 34 HIS ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20367 Z= 0.227 Angle : 0.712 11.150 27486 Z= 0.385 Chirality : 0.047 0.170 2970 Planarity : 0.004 0.050 3447 Dihedral : 12.763 176.746 2997 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 1.79 % Allowed : 12.41 % Favored : 85.80 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.00 (0.16), residues: 2457 helix: 0.06 (0.18), residues: 756 sheet: -2.00 (0.21), residues: 495 loop : -1.92 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 125 PHE 0.014 0.002 PHE D 104 TYR 0.029 0.002 TYR F 90 ARG 0.010 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7711 (tpp) cc_final: 0.7431 (tpp) REVERT: A 262 LEU cc_start: 0.8380 (mt) cc_final: 0.8104 (mt) REVERT: C 63 ASN cc_start: 0.7727 (m-40) cc_final: 0.7450 (m-40) REVERT: C 73 TYR cc_start: 0.7224 (m-80) cc_final: 0.6930 (m-80) REVERT: C 187 MET cc_start: 0.5526 (ptt) cc_final: 0.4929 (ptp) REVERT: C 202 MET cc_start: 0.8290 (mmm) cc_final: 0.8067 (mmm) REVERT: C 259 SER cc_start: 0.8502 (p) cc_final: 0.8280 (t) REVERT: D 94 THR cc_start: 0.9004 (p) cc_final: 0.8731 (t) REVERT: E 94 THR cc_start: 0.8406 (p) cc_final: 0.7978 (t) REVERT: E 148 MET cc_start: 0.7319 (mmm) cc_final: 0.6741 (mmm) REVERT: E 202 MET cc_start: 0.7713 (mmm) cc_final: 0.7395 (mmm) REVERT: E 262 LEU cc_start: 0.8433 (tp) cc_final: 0.8224 (tp) REVERT: F 73 TYR cc_start: 0.7386 (m-80) cc_final: 0.7169 (m-80) REVERT: F 106 LEU cc_start: 0.7410 (tp) cc_final: 0.7048 (tp) REVERT: F 202 MET cc_start: 0.8212 (mmm) cc_final: 0.7935 (tpp) REVERT: G 108 LEU cc_start: 0.7524 (mt) cc_final: 0.7106 (mt) REVERT: G 148 MET cc_start: 0.7194 (tpt) cc_final: 0.6812 (mmm) REVERT: G 202 MET cc_start: 0.7995 (mmt) cc_final: 0.7407 (tpt) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.3508 time to fit residues: 198.9270 Evaluate side-chains 270 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.0030 chunk 210 optimal weight: 0.0980 chunk 59 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20367 Z= 0.251 Angle : 0.706 9.772 27486 Z= 0.382 Chirality : 0.047 0.179 2970 Planarity : 0.004 0.046 3447 Dihedral : 12.590 177.298 2997 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 1.59 % Allowed : 12.70 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.10 (0.17), residues: 2457 helix: 0.16 (0.18), residues: 756 sheet: -2.07 (0.19), residues: 603 loop : -2.05 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 125 PHE 0.027 0.002 PHE H 270 TYR 0.033 0.002 TYR G 90 ARG 0.009 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7778 (tpp) cc_final: 0.7444 (tpp) REVERT: C 63 ASN cc_start: 0.7772 (m-40) cc_final: 0.7478 (m-40) REVERT: C 115 MET cc_start: 0.7014 (mmm) cc_final: 0.6658 (mmm) REVERT: C 187 MET cc_start: 0.5354 (ptt) cc_final: 0.4861 (ptp) REVERT: C 202 MET cc_start: 0.8316 (mmm) cc_final: 0.8035 (mmm) REVERT: E 94 THR cc_start: 0.8347 (p) cc_final: 0.7995 (t) REVERT: E 202 MET cc_start: 0.7707 (mmm) cc_final: 0.7421 (mmm) REVERT: F 202 MET cc_start: 0.8349 (mmm) cc_final: 0.7937 (tpp) REVERT: G 108 LEU cc_start: 0.7527 (mt) cc_final: 0.7130 (mt) REVERT: G 148 MET cc_start: 0.7034 (tpt) cc_final: 0.6800 (mmm) REVERT: H 45 MET cc_start: 0.8244 (mmm) cc_final: 0.7925 (tpp) REVERT: H 115 MET cc_start: 0.6478 (mmm) cc_final: 0.6081 (tpp) REVERT: I 1 MET cc_start: -0.0787 (tpt) cc_final: -0.2308 (tmm) REVERT: I 202 MET cc_start: 0.8112 (mmt) cc_final: 0.7793 (mmt) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3331 time to fit residues: 178.6769 Evaluate side-chains 247 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS G 23 GLN G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20367 Z= 0.342 Angle : 0.762 10.743 27486 Z= 0.406 Chirality : 0.048 0.190 2970 Planarity : 0.005 0.056 3447 Dihedral : 12.462 177.042 2997 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 1.55 % Allowed : 13.19 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.25 (0.16), residues: 2457 helix: -0.07 (0.18), residues: 756 sheet: -2.17 (0.21), residues: 513 loop : -2.10 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 190 PHE 0.018 0.002 PHE H 122 TYR 0.030 0.003 TYR F 90 ARG 0.007 0.001 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 ASN cc_start: 0.7767 (m-40) cc_final: 0.7528 (m-40) REVERT: E 94 THR cc_start: 0.8394 (p) cc_final: 0.8010 (t) REVERT: F 106 LEU cc_start: 0.7593 (tp) cc_final: 0.7356 (tp) REVERT: F 223 CYS cc_start: 0.8173 (t) cc_final: 0.7728 (t) REVERT: G 202 MET cc_start: 0.8393 (tpt) cc_final: 0.7554 (tpt) REVERT: H 45 MET cc_start: 0.8516 (mmm) cc_final: 0.7771 (mmm) REVERT: I 1 MET cc_start: -0.0820 (tpt) cc_final: -0.3123 (tmm) REVERT: I 115 MET cc_start: 0.7493 (mmm) cc_final: 0.7174 (mmm) REVERT: I 202 MET cc_start: 0.8136 (mmt) cc_final: 0.7773 (mmt) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3377 time to fit residues: 168.6501 Evaluate side-chains 241 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20367 Z= 0.195 Angle : 0.704 14.215 27486 Z= 0.375 Chirality : 0.047 0.196 2970 Planarity : 0.004 0.058 3447 Dihedral : 12.346 164.649 2997 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 1.51 % Allowed : 11.97 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -1.78 (0.16), residues: 2457 helix: 0.57 (0.19), residues: 693 sheet: -1.90 (0.21), residues: 504 loop : -1.88 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 125 PHE 0.028 0.001 PHE F 270 TYR 0.038 0.002 TYR D 18 ARG 0.009 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6971 (ttm) cc_final: 0.6620 (tmm) REVERT: A 215 ILE cc_start: 0.9065 (mm) cc_final: 0.8658 (tp) REVERT: C 63 ASN cc_start: 0.7669 (m-40) cc_final: 0.7396 (m-40) REVERT: C 187 MET cc_start: 0.5002 (ptt) cc_final: 0.4528 (ptp) REVERT: C 202 MET cc_start: 0.8046 (mmm) cc_final: 0.7534 (mmm) REVERT: D 191 THR cc_start: 0.8421 (m) cc_final: 0.8072 (m) REVERT: E 94 THR cc_start: 0.8378 (p) cc_final: 0.7991 (t) REVERT: E 202 MET cc_start: 0.7540 (mmm) cc_final: 0.7203 (mmm) REVERT: F 98 GLU cc_start: 0.6909 (pt0) cc_final: 0.6628 (pt0) REVERT: G 108 LEU cc_start: 0.7561 (mt) cc_final: 0.7267 (mt) REVERT: G 148 MET cc_start: 0.6896 (tpt) cc_final: 0.6686 (mmm) REVERT: G 202 MET cc_start: 0.8275 (tpt) cc_final: 0.7780 (tpt) REVERT: H 45 MET cc_start: 0.8445 (mmm) cc_final: 0.7547 (tpp) REVERT: I 1 MET cc_start: -0.0952 (tpt) cc_final: -0.3122 (tmm) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3240 time to fit residues: 179.1882 Evaluate side-chains 264 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN G 23 GLN G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20367 Z= 0.217 Angle : 0.697 8.634 27486 Z= 0.374 Chirality : 0.047 0.182 2970 Planarity : 0.004 0.062 3447 Dihedral : 12.248 167.546 2997 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 1.55 % Allowed : 12.13 % Favored : 86.32 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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 (0.17), residues: 2457 helix: 0.52 (0.19), residues: 693 sheet: -1.91 (0.19), residues: 612 loop : -2.01 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS I 125 PHE 0.046 0.002 PHE F 270 TYR 0.029 0.002 TYR A 18 ARG 0.009 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9074 (mm) cc_final: 0.8687 (tp) REVERT: C 63 ASN cc_start: 0.7688 (m-40) cc_final: 0.7196 (m-40) REVERT: C 73 TYR cc_start: 0.7187 (m-80) cc_final: 0.6680 (m-80) REVERT: C 187 MET cc_start: 0.4959 (ptt) cc_final: 0.4443 (ptp) REVERT: C 202 MET cc_start: 0.8073 (mmm) cc_final: 0.7510 (mmm) REVERT: E 94 THR cc_start: 0.8311 (p) cc_final: 0.7970 (t) REVERT: E 202 MET cc_start: 0.7566 (mmm) cc_final: 0.7211 (mmm) REVERT: F 202 MET cc_start: 0.7773 (tpp) cc_final: 0.7387 (mmm) REVERT: G 108 LEU cc_start: 0.7633 (mt) cc_final: 0.7280 (mt) REVERT: G 202 MET cc_start: 0.8218 (tpt) cc_final: 0.7701 (tpt) REVERT: H 45 MET cc_start: 0.8465 (mmm) cc_final: 0.7600 (tpp) REVERT: I 1 MET cc_start: -0.0979 (tpt) cc_final: -0.3088 (tmm) REVERT: I 115 MET cc_start: 0.6444 (mmm) cc_final: 0.6198 (mmm) REVERT: I 202 MET cc_start: 0.8182 (mmt) cc_final: 0.7898 (mmt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3336 time to fit residues: 175.5787 Evaluate side-chains 255 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 171 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 197 optimal weight: 0.2980 chunk 206 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN G 23 GLN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 HIS ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20367 Z= 0.234 Angle : 0.716 7.851 27486 Z= 0.386 Chirality : 0.048 0.275 2970 Planarity : 0.004 0.066 3447 Dihedral : 12.217 165.693 2997 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 1.34 % Allowed : 12.29 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -1.93 (0.17), residues: 2457 helix: 0.42 (0.19), residues: 684 sheet: -1.82 (0.19), residues: 675 loop : -1.97 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 125 PHE 0.032 0.002 PHE F 270 TYR 0.037 0.002 TYR F 56 ARG 0.008 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9037 (mm) cc_final: 0.8742 (tp) REVERT: B 202 MET cc_start: 0.7244 (mmp) cc_final: 0.6650 (mmp) REVERT: C 63 ASN cc_start: 0.7716 (m-40) cc_final: 0.7159 (m-40) REVERT: C 73 TYR cc_start: 0.7236 (m-80) cc_final: 0.6742 (m-80) REVERT: C 187 MET cc_start: 0.4880 (ptt) cc_final: 0.4310 (ptp) REVERT: C 202 MET cc_start: 0.8033 (mmm) cc_final: 0.7521 (mmm) REVERT: D 71 GLN cc_start: 0.6977 (mt0) cc_final: 0.6656 (mt0) REVERT: E 94 THR cc_start: 0.8320 (p) cc_final: 0.7930 (t) REVERT: E 202 MET cc_start: 0.7584 (mmm) cc_final: 0.7193 (mmm) REVERT: F 45 MET cc_start: 0.6743 (tpp) cc_final: 0.6313 (mmm) REVERT: F 115 MET cc_start: 0.7906 (mmm) cc_final: 0.7570 (tpp) REVERT: F 202 MET cc_start: 0.7720 (tpp) cc_final: 0.7340 (mmm) REVERT: G 202 MET cc_start: 0.8198 (tpt) cc_final: 0.7732 (tpt) REVERT: H 45 MET cc_start: 0.8506 (mmm) cc_final: 0.7463 (tpp) REVERT: I 1 MET cc_start: -0.0818 (tpt) cc_final: -0.2905 (tmm) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.3352 time to fit residues: 171.0051 Evaluate side-chains 259 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 40.0000 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 222 optimal weight: 0.0670 chunk 192 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN G 23 GLN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20367 Z= 0.208 Angle : 0.709 8.672 27486 Z= 0.380 Chirality : 0.048 0.219 2970 Planarity : 0.004 0.067 3447 Dihedral : 12.172 164.051 2997 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 1.30 % Allowed : 11.88 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -1.98 (0.17), residues: 2457 helix: 0.34 (0.19), residues: 684 sheet: -1.87 (0.20), residues: 639 loop : -1.98 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS I 125 PHE 0.044 0.002 PHE F 270 TYR 0.040 0.002 TYR F 56 ARG 0.007 0.001 ARG G 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7552 (mpp) cc_final: 0.6801 (mpp) REVERT: A 107 ILE cc_start: 0.8919 (mm) cc_final: 0.8693 (mm) REVERT: A 187 MET cc_start: 0.4414 (mtm) cc_final: 0.3677 (mtt) REVERT: A 211 THR cc_start: 0.8560 (p) cc_final: 0.8343 (p) REVERT: A 215 ILE cc_start: 0.9064 (mm) cc_final: 0.8735 (tp) REVERT: B 202 MET cc_start: 0.7273 (mmp) cc_final: 0.6717 (mmp) REVERT: C 63 ASN cc_start: 0.7702 (m-40) cc_final: 0.7164 (m-40) REVERT: C 73 TYR cc_start: 0.7209 (m-80) cc_final: 0.6677 (m-80) REVERT: C 187 MET cc_start: 0.4776 (ptt) cc_final: 0.4262 (ptp) REVERT: C 202 MET cc_start: 0.8014 (mmm) cc_final: 0.7523 (mmm) REVERT: D 71 GLN cc_start: 0.6973 (mt0) cc_final: 0.6653 (mt0) REVERT: D 115 MET cc_start: 0.7676 (mmm) cc_final: 0.6717 (tpp) REVERT: E 94 THR cc_start: 0.8330 (p) cc_final: 0.7922 (t) REVERT: E 202 MET cc_start: 0.7534 (mmm) cc_final: 0.7172 (mmm) REVERT: F 187 MET cc_start: 0.6597 (mtm) cc_final: 0.6355 (mtt) REVERT: F 202 MET cc_start: 0.7658 (tpp) cc_final: 0.7274 (mmm) REVERT: G 202 MET cc_start: 0.8187 (tpt) cc_final: 0.7787 (tpt) REVERT: H 45 MET cc_start: 0.8509 (mmm) cc_final: 0.7380 (tpp) REVERT: I 1 MET cc_start: -0.0982 (tpt) cc_final: -0.2968 (tmm) REVERT: I 202 MET cc_start: 0.8023 (mmt) cc_final: 0.7740 (mmt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.3251 time to fit residues: 166.8362 Evaluate side-chains 262 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 24 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052308 restraints weight = 96064.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054217 restraints weight = 51767.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055504 restraints weight = 32622.294| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.7383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20367 Z= 0.187 Angle : 0.712 9.697 27486 Z= 0.381 Chirality : 0.048 0.204 2970 Planarity : 0.004 0.066 3447 Dihedral : 12.159 165.097 2997 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.33 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % 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: -2.02 (0.17), residues: 2457 helix: 0.30 (0.19), residues: 684 sheet: -1.91 (0.19), residues: 693 loop : -1.95 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS I 125 PHE 0.035 0.002 PHE E 270 TYR 0.039 0.002 TYR F 56 ARG 0.007 0.001 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4269.02 seconds wall clock time: 78 minutes 18.56 seconds (4698.56 seconds total)