Starting phenix.real_space_refine on Sun Dec 10 16:17:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7e_27228/12_2023/8d7e_27228.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7e_27228/12_2023/8d7e_27228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7e_27228/12_2023/8d7e_27228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7e_27228/12_2023/8d7e_27228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7e_27228/12_2023/8d7e_27228.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7e_27228/12_2023/8d7e_27228.pdb" } resolution = 2.93 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6044 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5654 2.51 5 N 1512 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 24": "NH1" <-> "NH2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "G GLU 1": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 166": not complete - not flipped Residue "G GLU 166": not complete - not flipped Residue "G TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 166": not complete - not flipped Residue "E GLU 166": not complete - not flipped Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 10": "OD1" <-> "OD2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 151": "OD1" <-> "OD2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8959 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "G" Number of atoms: 1649 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1649 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Chain: "F" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1654 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1646 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.07, per 1000 atoms: 0.57 Number of scatterers: 8959 At special positions: 0 Unit cell: (84.15, 125.8, 165.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1759 8.00 N 1512 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 215 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 1 " - " ASN C 190 " " NAG B 1 " - " ASN C 70 " " NAG H 1 " - " ASN C 60 " " NAG I 1 " - " ASN C 142 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 26 sheets defined 6.4% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.925A pdb=" N SER G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.205A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 188 removed outlier: 3.631A pdb=" N GLU G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 188' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.590A pdb=" N THR F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.856A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 194 removed outlier: 4.055A pdb=" N GLY F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.059A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.602A pdb=" N LEU E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.560A pdb=" N HIS E 190 " --> pdb=" O ASP E 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.576A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 37 removed outlier: 6.108A pdb=" N HIS C 32 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS C 104 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN C 34 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY C 106 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C 36 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU C 97 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS C 91 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 99 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.682A pdb=" N VAL C 42 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 117 removed outlier: 3.544A pdb=" N HIS C 130 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 151 removed outlier: 3.699A pdb=" N HIS C 147 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 140 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 213 removed outlier: 3.569A pdb=" N VAL C 211 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 225 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 224 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 265 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA8, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.547A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 19 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE G 72 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.583A pdb=" N TYR G 88 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AB2, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.557A pdb=" N ASN G 138 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 150 removed outlier: 4.099A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 198 " --> pdb=" O LYS G 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.562A pdb=" N ALA F 92 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 97 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS F 35 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.474A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.474A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 158 removed outlier: 3.784A pdb=" N THR F 155 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F 203 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS F 200 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7 removed outlier: 11.818A pdb=" N CYS E 23 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N THR E 74 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N ALA E 25 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 12.016A pdb=" N THR E 72 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLN E 27 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP E 70 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.511A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.763A pdb=" N LYS E 150 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.930A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS D 96 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP D 110 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA D 98 " --> pdb=" O GLN D 108 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.930A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.652A pdb=" N SER D 187 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.231A pdb=" N TYR D 201 " --> pdb=" O VAL D 218 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2662 1.33 - 1.46: 1935 1.46 - 1.58: 4555 1.58 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 9194 Sorted by residual: bond pdb=" C ILE C 278 " pdb=" O ILE C 278 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.04e-02 9.25e+03 5.72e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C ARG D 16 " pdb=" O ARG D 16 " ideal model delta sigma weight residual 1.234 1.215 0.020 1.28e-02 6.10e+03 2.36e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 ... (remaining 9189 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 430 107.46 - 114.09: 5197 114.09 - 120.72: 3286 120.72 - 127.35: 3490 127.35 - 133.98: 130 Bond angle restraints: 12533 Sorted by residual: angle pdb=" N ALA C 296 " pdb=" CA ALA C 296 " pdb=" C ALA C 296 " ideal model delta sigma weight residual 107.88 112.34 -4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" CA CYS C 154 " pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " ideal model delta sigma weight residual 114.40 121.59 -7.19 2.30e+00 1.89e-01 9.77e+00 angle pdb=" N LYS D 208 " pdb=" CA LYS D 208 " pdb=" C LYS D 208 " ideal model delta sigma weight residual 109.81 116.48 -6.67 2.21e+00 2.05e-01 9.11e+00 angle pdb=" C HIS F 204 " pdb=" N LYS F 205 " pdb=" CA LYS F 205 " ideal model delta sigma weight residual 120.09 123.47 -3.38 1.25e+00 6.40e-01 7.31e+00 angle pdb=" C LYS D 208 " pdb=" N PRO D 209 " pdb=" CA PRO D 209 " ideal model delta sigma weight residual 118.97 116.39 2.58 1.04e+00 9.25e-01 6.15e+00 ... (remaining 12528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 5495 33.93 - 67.86: 73 67.86 - 101.80: 10 101.80 - 135.73: 1 135.73 - 169.66: 1 Dihedral angle restraints: 5580 sinusoidal: 2260 harmonic: 3320 Sorted by residual: dihedral pdb=" CB GLU E 166 " pdb=" CG GLU E 166 " pdb=" CD GLU E 166 " pdb=" OE1 GLU E 166 " ideal model delta sinusoidal sigma weight residual 0.00 169.66 -169.66 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB CYS G 215 " pdb=" SG CYS G 215 " pdb=" SG CYS F 131 " pdb=" CB CYS F 131 " ideal model delta sinusoidal sigma weight residual -86.00 -49.68 -36.32 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CB GLU G 166 " pdb=" CG GLU G 166 " pdb=" CD GLU G 166 " pdb=" OE1 GLU G 166 " ideal model delta sinusoidal sigma weight residual 0.00 104.32 -104.32 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 5577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1230 0.057 - 0.113: 177 0.113 - 0.170: 9 0.170 - 0.226: 0 0.226 - 0.283: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA LYS D 208 " pdb=" N LYS D 208 " pdb=" C LYS D 208 " pdb=" CB LYS D 208 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1415 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 95 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO E 96 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 153 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO D 154 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 154 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 154 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 95 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO G 96 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " -0.017 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1916 2.79 - 3.31: 7168 3.31 - 3.84: 14328 3.84 - 4.37: 16082 4.37 - 4.90: 29061 Nonbonded interactions: 68555 Sorted by model distance: nonbonded pdb=" OH TYR G 37 " pdb=" OE1 GLN G 90 " model vdw 2.257 2.440 nonbonded pdb=" OD1 ASP F 73 " pdb=" OG SER F 75 " model vdw 2.260 2.440 nonbonded pdb=" O HIS C 83 " pdb=" OH TYR C 87 " model vdw 2.294 2.440 nonbonded pdb=" O PRO D 192 " pdb=" OG SER D 195 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASP D 54 " pdb=" OG SER D 56 " model vdw 2.334 2.440 ... (remaining 68550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'D' and (resid 1 through 9 or resid 11 through 22 or resid 24 through 30 \ or resid 34 through 39 or resid 41 through 48 or resid 51 or resid 54 through 55 \ or resid 58 or resid 60 or resid 62 through 78 or resid 81 through 87 or resid \ 89 through 91 or resid 94 through 97 or resid 103 or resid 107 or resid 110 thro \ ugh 114 or resid 116 through 220)) selection = (chain 'F' and (resid 1 through 9 or resid 11 through 22 or resid 24 through 30 \ or resid 34 through 39 or resid 41 through 48 or resid 51 or resid 54 through 55 \ or resid 58 or resid 60 or resid 62 through 78 or resid 81 through 87 or resid \ 89 through 91 or resid 94 through 97 or resid 101 or resid 104 or resid 107 thro \ ugh 111 or resid 113 through 132 or resid 139 through 217)) } ncs_group { reference = (chain 'E' and (resid 2 or resid 5 through 8 or resid 11 through 12 or resid 14 \ or resid 16 or resid 18 or resid 20 or resid 23 through 28 or resid 30 through 3 \ 3 or resid 35 through 41 or resid 43 through 44 or resid 46 through 49 or resid \ 51 through 53 or resid 57 or resid 59 or resid 61 through 76 or resid 78 or resi \ d 80 through 84 or resid 86 through 90 or resid 93 or resid 95 or resid 98 throu \ gh 103 or resid 106 through 215)) selection = (chain 'G' and (resid 2 or resid 5 through 8 or resid 11 through 12 or resid 14 \ or resid 16 or resid 18 or resid 20 or resid 23 through 28 or resid 30 through 3 \ 1 or resid 33 through 34 or resid 36 through 42 or resid 44 through 45 or resid \ 47 through 50 or resid 52 through 54 or resid 58 or resid 60 or resid 62 through \ 77 or resid 79 or resid 81 through 85 or resid 87 through 91 or resid 94 or res \ id 96 or resid 98 through 103 or resid 106 through 215)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 8.520 Check model and map are aligned: 0.150 Set scattering table: 0.070 Process input model: 26.550 Find NCS groups from input model: 0.440 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.002 0.047 9194 Z= 0.154 Angle : 0.492 7.496 12533 Z= 0.264 Chirality : 0.041 0.283 1418 Planarity : 0.004 0.038 1593 Dihedral : 11.955 169.662 3407 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.70 % Allowed : 16.62 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.23), residues: 1131 helix: -4.06 (0.45), residues: 28 sheet: -0.79 (0.23), residues: 494 loop : -1.98 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 293 HIS 0.002 0.000 HIS D 207 PHE 0.004 0.001 PHE F 126 TYR 0.018 0.001 TYR C 276 ARG 0.002 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.061 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 157 average time/residue: 1.0396 time to fit residues: 175.7347 Evaluate side-chains 103 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0797 time to fit residues: 1.5699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 HIS C 100 GLN C 119 ASN C 209 ASN C 256 HIS G 27 GLN F 57 ASN F 77 ASN F 175 GLN F 201 ASN E 27 GLN E 34 ASN E 148 GLN D 77 ASN D 99 GLN D 178 GLN D 204 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9194 Z= 0.243 Angle : 0.611 8.268 12533 Z= 0.305 Chirality : 0.046 0.183 1418 Planarity : 0.005 0.058 1593 Dihedral : 3.795 18.670 1400 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.40 % Allowed : 19.82 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1131 helix: -3.34 (0.61), residues: 29 sheet: -0.22 (0.22), residues: 528 loop : -1.15 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 101 HIS 0.006 0.002 HIS C 104 PHE 0.014 0.002 PHE G 119 TYR 0.015 0.002 TYR F 95 ARG 0.004 0.001 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 103 time to evaluate : 0.939 Fit side-chains outliers start: 44 outliers final: 23 residues processed: 139 average time/residue: 1.1216 time to fit residues: 168.1300 Evaluate side-chains 114 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.1285 time to fit residues: 2.2518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN F 77 ASN F 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9194 Z= 0.332 Angle : 0.638 9.522 12533 Z= 0.323 Chirality : 0.047 0.173 1418 Planarity : 0.005 0.047 1593 Dihedral : 4.419 17.511 1400 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.81 % Allowed : 19.82 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1131 helix: -3.37 (0.56), residues: 29 sheet: 0.18 (0.23), residues: 519 loop : -0.99 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 101 HIS 0.009 0.002 HIS C 99 PHE 0.014 0.002 PHE F 100 TYR 0.017 0.002 TYR F 95 ARG 0.004 0.001 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 95 time to evaluate : 0.909 Fit side-chains outliers start: 68 outliers final: 44 residues processed: 145 average time/residue: 1.0528 time to fit residues: 164.6764 Evaluate side-chains 136 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 92 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 34 residues processed: 10 average time/residue: 0.8808 time to fit residues: 10.8938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN F 77 ASN E 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9194 Z= 0.356 Angle : 0.646 9.736 12533 Z= 0.323 Chirality : 0.047 0.175 1418 Planarity : 0.005 0.042 1593 Dihedral : 4.671 19.097 1400 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.71 % Allowed : 20.62 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1131 helix: -3.22 (0.61), residues: 29 sheet: 0.37 (0.23), residues: 526 loop : -0.90 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 101 HIS 0.008 0.002 HIS C 99 PHE 0.015 0.002 PHE C 141 TYR 0.020 0.002 TYR D 152 ARG 0.007 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 86 time to evaluate : 0.946 Fit side-chains outliers start: 67 outliers final: 49 residues processed: 140 average time/residue: 1.1103 time to fit residues: 167.2361 Evaluate side-chains 132 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 83 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 7 average time/residue: 1.0601 time to fit residues: 9.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9194 Z= 0.219 Angle : 0.574 9.000 12533 Z= 0.287 Chirality : 0.044 0.156 1418 Planarity : 0.005 0.040 1593 Dihedral : 4.542 20.002 1400 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.21 % Allowed : 21.42 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1131 helix: -3.08 (0.65), residues: 29 sheet: 0.47 (0.23), residues: 528 loop : -0.77 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 101 HIS 0.005 0.001 HIS C 99 PHE 0.009 0.001 PHE E 99 TYR 0.019 0.001 TYR D 152 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 85 time to evaluate : 1.034 Fit side-chains outliers start: 62 outliers final: 49 residues processed: 137 average time/residue: 0.9717 time to fit residues: 144.4240 Evaluate side-chains 127 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 78 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 44 residues processed: 6 average time/residue: 0.7552 time to fit residues: 6.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN D 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9194 Z= 0.285 Angle : 0.601 9.655 12533 Z= 0.301 Chirality : 0.045 0.164 1418 Planarity : 0.005 0.041 1593 Dihedral : 4.790 20.936 1400 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 6.21 % Allowed : 21.82 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1131 helix: -3.24 (0.55), residues: 35 sheet: 0.53 (0.23), residues: 527 loop : -0.75 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 101 HIS 0.007 0.001 HIS C 99 PHE 0.010 0.001 PHE E 99 TYR 0.018 0.002 TYR F 95 ARG 0.004 0.000 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 80 time to evaluate : 1.087 Fit side-chains outliers start: 62 outliers final: 48 residues processed: 130 average time/residue: 0.9358 time to fit residues: 132.8036 Evaluate side-chains 129 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 81 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 6 average time/residue: 0.6047 time to fit residues: 5.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.0070 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 209 ASN F 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9194 Z= 0.144 Angle : 0.535 8.505 12533 Z= 0.265 Chirality : 0.043 0.176 1418 Planarity : 0.004 0.042 1593 Dihedral : 4.476 23.731 1400 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.61 % Allowed : 22.52 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1131 helix: -3.00 (0.59), residues: 34 sheet: 0.62 (0.23), residues: 532 loop : -0.62 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 101 HIS 0.003 0.001 HIS C 99 PHE 0.008 0.001 PHE C 125 TYR 0.018 0.001 TYR D 152 ARG 0.004 0.000 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 87 time to evaluate : 1.061 Fit side-chains outliers start: 56 outliers final: 47 residues processed: 137 average time/residue: 0.8927 time to fit residues: 133.9349 Evaluate side-chains 129 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 82 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 4 average time/residue: 0.8198 time to fit residues: 4.8256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN F 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9194 Z= 0.288 Angle : 0.616 10.121 12533 Z= 0.307 Chirality : 0.046 0.231 1418 Planarity : 0.005 0.042 1593 Dihedral : 4.930 30.462 1400 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.51 % Allowed : 23.32 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1131 helix: -2.94 (0.61), residues: 34 sheet: 0.63 (0.23), residues: 539 loop : -0.62 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 101 HIS 0.006 0.001 HIS C 99 PHE 0.010 0.001 PHE F 100 TYR 0.025 0.002 TYR D 152 ARG 0.006 0.000 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 82 time to evaluate : 0.948 Fit side-chains outliers start: 55 outliers final: 51 residues processed: 132 average time/residue: 0.9560 time to fit residues: 137.5711 Evaluate side-chains 132 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 81 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 48 residues processed: 5 average time/residue: 1.0761 time to fit residues: 7.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN F 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9194 Z= 0.265 Angle : 0.612 9.662 12533 Z= 0.307 Chirality : 0.046 0.393 1418 Planarity : 0.005 0.042 1593 Dihedral : 5.100 37.233 1400 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.41 % Allowed : 23.72 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1131 helix: -2.90 (0.62), residues: 34 sheet: 0.60 (0.23), residues: 539 loop : -0.61 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 101 HIS 0.006 0.001 HIS C 99 PHE 0.010 0.001 PHE E 99 TYR 0.023 0.002 TYR D 152 ARG 0.003 0.000 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 83 time to evaluate : 0.936 Fit side-chains outliers start: 54 outliers final: 53 residues processed: 131 average time/residue: 0.9580 time to fit residues: 136.2715 Evaluate side-chains 136 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 83 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 50 residues processed: 5 average time/residue: 0.6998 time to fit residues: 5.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN F 77 ASN D 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9194 Z= 0.337 Angle : 0.637 10.247 12533 Z= 0.320 Chirality : 0.047 0.231 1418 Planarity : 0.005 0.042 1593 Dihedral : 5.165 45.979 1400 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.71 % Allowed : 23.72 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1131 helix: -2.94 (0.61), residues: 34 sheet: 0.44 (0.22), residues: 550 loop : -0.57 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 101 HIS 0.007 0.001 HIS C 99 PHE 0.012 0.002 PHE F 100 TYR 0.022 0.002 TYR D 152 ARG 0.004 0.000 ARG D 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 79 time to evaluate : 1.133 Fit side-chains outliers start: 57 outliers final: 50 residues processed: 129 average time/residue: 0.9524 time to fit residues: 133.6783 Evaluate side-chains 129 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 79 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 48 residues processed: 3 average time/residue: 0.7971 time to fit residues: 3.8771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106720 restraints weight = 11138.006| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.24 r_work: 0.3044 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9194 Z= 0.304 Angle : 0.616 9.912 12533 Z= 0.309 Chirality : 0.046 0.254 1418 Planarity : 0.005 0.042 1593 Dihedral : 5.010 38.663 1400 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.90 % Allowed : 24.52 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1131 helix: -2.96 (0.60), residues: 35 sheet: 0.47 (0.22), residues: 549 loop : -0.52 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 101 HIS 0.006 0.001 HIS C 99 PHE 0.012 0.001 PHE C 141 TYR 0.022 0.002 TYR D 152 ARG 0.004 0.000 ARG D 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3389.29 seconds wall clock time: 61 minutes 6.03 seconds (3666.03 seconds total)