Starting phenix.real_space_refine on Wed Feb 21 17:19:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efy_28107/02_2024/8efy_28107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efy_28107/02_2024/8efy_28107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efy_28107/02_2024/8efy_28107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efy_28107/02_2024/8efy_28107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efy_28107/02_2024/8efy_28107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efy_28107/02_2024/8efy_28107_updated.pdb" } resolution = 3.16 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= 0.009 sd= 0.092 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: 6 Type Number sf(0) Gaussians P 124 5.49 5 Mg 8 5.21 5 S 52 5.16 5 C 19461 2.51 5 N 5664 2.21 5 O 5965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31274 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2446 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2428 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2363 Classifications: {'peptide': 302} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2415 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2420 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2409 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 490 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "H" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2442 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2453 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2381 Classifications: {'peptide': 304} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2415 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2399 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2420 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "P" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.64, per 1000 atoms: 0.50 Number of scatterers: 31274 At special positions: 0 Unit cell: (147.96, 163.08, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 124 15.00 Mg 8 11.99 O 5965 8.00 N 5664 7.00 C 19461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.34 Conformation dependent library (CDL) restraints added in 5.3 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 33 sheets defined 47.6% alpha, 8.8% beta 42 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 14.07 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 removed outlier: 3.906A pdb=" N VAL A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 62 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 104 through 107 No H-bonds generated for 'chain 'A' and resid 104 through 107' Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'B' and resid 18 through 33 removed outlier: 3.778A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.937A pdb=" N GLU B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 204 through 221 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 268 through 274 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'C' and resid 18 through 33 removed outlier: 3.827A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 80 through 86 removed outlier: 4.068A pdb=" N LEU C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 112 through 115 No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.768A pdb=" N ARG C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 204 through 221 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.948A pdb=" N LYS D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 79 through 85 Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.910A pdb=" N HIS D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 153 through 158 removed outlier: 3.779A pdb=" N ARG D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 184 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 204 through 220 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 278 through 284 Processing helix chain 'D' and resid 286 through 289 No H-bonds generated for 'chain 'D' and resid 286 through 289' Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 51 through 62 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 104 through 115 removed outlier: 3.578A pdb=" N HIS E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.667A pdb=" N ARG E 158 " --> pdb=" O PRO E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 184 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 204 through 221 Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'F' and resid 18 through 34 removed outlier: 3.879A pdb=" N LYS F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 107 through 115 removed outlier: 3.649A pdb=" N TYR F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Proline residue: F 112 - end of helix Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 170 through 184 Processing helix chain 'F' and resid 190 through 199 Processing helix chain 'F' and resid 204 through 220 removed outlier: 3.771A pdb=" N VAL F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 Processing helix chain 'F' and resid 247 through 260 removed outlier: 3.844A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 270 No H-bonds generated for 'chain 'F' and resid 267 through 270' Processing helix chain 'F' and resid 280 through 283 No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'I' and resid 18 through 34 removed outlier: 3.997A pdb=" N VAL I 26 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 62 Processing helix chain 'I' and resid 77 through 86 Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 104 through 115 removed outlier: 3.866A pdb=" N LEU I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Proline residue: I 112 - end of helix Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 153 through 158 Processing helix chain 'I' and resid 170 through 184 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 204 through 221 Processing helix chain 'I' and resid 228 through 238 Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 281 through 284 No H-bonds generated for 'chain 'I' and resid 281 through 284' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 306 through 311 Processing helix chain 'J' and resid 18 through 33 removed outlier: 3.831A pdb=" N LYS J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL J 26 " --> pdb=" O GLN J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 62 Processing helix chain 'J' and resid 79 through 86 Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 104 through 107 No H-bonds generated for 'chain 'J' and resid 104 through 107' Processing helix chain 'J' and resid 126 through 128 No H-bonds generated for 'chain 'J' and resid 126 through 128' Processing helix chain 'J' and resid 148 through 150 No H-bonds generated for 'chain 'J' and resid 148 through 150' Processing helix chain 'J' and resid 153 through 157 Processing helix chain 'J' and resid 170 through 184 Processing helix chain 'J' and resid 190 through 199 Processing helix chain 'J' and resid 204 through 221 Processing helix chain 'J' and resid 228 through 238 Processing helix chain 'J' and resid 247 through 258 Processing helix chain 'J' and resid 267 through 274 Processing helix chain 'J' and resid 278 through 283 Processing helix chain 'J' and resid 286 through 292 Processing helix chain 'J' and resid 306 through 312 Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.932A pdb=" N LYS K 23 " --> pdb=" O ARG K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 61 Processing helix chain 'K' and resid 78 through 87 removed outlier: 3.809A pdb=" N ALA K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 101 No H-bonds generated for 'chain 'K' and resid 99 through 101' Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 115 No H-bonds generated for 'chain 'K' and resid 112 through 115' Processing helix chain 'K' and resid 153 through 158 removed outlier: 3.666A pdb=" N ARG K 158 " --> pdb=" O PRO K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 184 Processing helix chain 'K' and resid 190 through 199 Processing helix chain 'K' and resid 204 through 221 Processing helix chain 'K' and resid 228 through 238 Processing helix chain 'K' and resid 247 through 258 Processing helix chain 'K' and resid 267 through 273 Processing helix chain 'K' and resid 278 through 283 Processing helix chain 'K' and resid 286 through 292 Processing helix chain 'K' and resid 306 through 311 Processing helix chain 'L' and resid 18 through 33 removed outlier: 3.869A pdb=" N LYS L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 62 Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 99 through 101 No H-bonds generated for 'chain 'L' and resid 99 through 101' Processing helix chain 'L' and resid 104 through 109 removed outlier: 3.908A pdb=" N HIS L 109 " --> pdb=" O GLN L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 115 Processing helix chain 'L' and resid 148 through 150 No H-bonds generated for 'chain 'L' and resid 148 through 150' Processing helix chain 'L' and resid 153 through 158 removed outlier: 3.560A pdb=" N ARG L 158 " --> pdb=" O PRO L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 184 Processing helix chain 'L' and resid 190 through 198 Processing helix chain 'L' and resid 204 through 220 Processing helix chain 'L' and resid 228 through 237 Processing helix chain 'L' and resid 247 through 258 Processing helix chain 'L' and resid 267 through 274 Processing helix chain 'L' and resid 278 through 284 Processing helix chain 'L' and resid 286 through 289 No H-bonds generated for 'chain 'L' and resid 286 through 289' Processing helix chain 'L' and resid 306 through 311 Processing helix chain 'M' and resid 21 through 34 Processing helix chain 'M' and resid 51 through 62 Processing helix chain 'M' and resid 71 through 73 No H-bonds generated for 'chain 'M' and resid 71 through 73' Processing helix chain 'M' and resid 79 through 86 removed outlier: 3.908A pdb=" N ASN M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.567A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS M 109 " --> pdb=" O GLN M 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU M 110 " --> pdb=" O ALA M 106 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Proline residue: M 112 - end of helix Processing helix chain 'M' and resid 148 through 150 No H-bonds generated for 'chain 'M' and resid 148 through 150' Processing helix chain 'M' and resid 153 through 158 removed outlier: 3.660A pdb=" N ARG M 158 " --> pdb=" O PRO M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 184 Processing helix chain 'M' and resid 190 through 199 Processing helix chain 'M' and resid 204 through 221 Processing helix chain 'M' and resid 228 through 238 Processing helix chain 'M' and resid 247 through 260 Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 286 through 291 Processing helix chain 'M' and resid 307 through 311 Processing helix chain 'N' and resid 18 through 34 removed outlier: 3.950A pdb=" N LYS N 23 " --> pdb=" O ARG N 19 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 62 Processing helix chain 'N' and resid 79 through 86 Processing helix chain 'N' and resid 99 through 101 No H-bonds generated for 'chain 'N' and resid 99 through 101' Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.666A pdb=" N TYR N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) Proline residue: N 112 - end of helix Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 170 through 184 Processing helix chain 'N' and resid 190 through 199 Processing helix chain 'N' and resid 204 through 220 removed outlier: 3.735A pdb=" N VAL N 220 " --> pdb=" O ASP N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 238 Processing helix chain 'N' and resid 247 through 260 removed outlier: 3.868A pdb=" N ARG N 259 " --> pdb=" O VAL N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 272 removed outlier: 4.024A pdb=" N ALA N 271 " --> pdb=" O LEU N 267 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 267 through 272' Processing helix chain 'N' and resid 280 through 283 No H-bonds generated for 'chain 'N' and resid 280 through 283' Processing helix chain 'N' and resid 286 through 292 Processing helix chain 'N' and resid 306 through 311 Processing sheet with id= A, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= B, first strand: chain 'A' and resid 118 through 123 Processing sheet with id= C, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= D, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.903A pdb=" N GLY B 45 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 118 through 122 Processing sheet with id= F, first strand: chain 'B' and resid 296 through 298 Processing sheet with id= G, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= H, first strand: chain 'C' and resid 295 through 298 Processing sheet with id= I, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= J, first strand: chain 'D' and resid 118 through 122 Processing sheet with id= K, first strand: chain 'D' and resid 296 through 298 Processing sheet with id= L, first strand: chain 'E' and resid 142 through 144 removed outlier: 6.857A pdb=" N LEU E 41 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE E 161 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE E 44 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU E 163 " --> pdb=" O PHE E 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 118 through 121 removed outlier: 4.099A pdb=" N ILE E 132 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 296 through 298 Processing sheet with id= O, first strand: chain 'F' and resid 161 through 163 Processing sheet with id= P, first strand: chain 'F' and resid 118 through 121 Processing sheet with id= Q, first strand: chain 'F' and resid 295 through 297 Processing sheet with id= R, first strand: chain 'I' and resid 161 through 165 Processing sheet with id= S, first strand: chain 'I' and resid 118 through 123 Processing sheet with id= T, first strand: chain 'I' and resid 295 through 297 Processing sheet with id= U, first strand: chain 'J' and resid 161 through 165 removed outlier: 3.952A pdb=" N GLY J 45 " --> pdb=" O THR J 145 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 118 through 123 Processing sheet with id= W, first strand: chain 'J' and resid 296 through 298 Processing sheet with id= X, first strand: chain 'K' and resid 161 through 164 removed outlier: 6.468A pdb=" N ASP K 92 " --> pdb=" O THR K 140 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE K 142 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU K 94 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA K 144 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE K 96 " --> pdb=" O ALA K 144 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 295 through 298 Processing sheet with id= Z, first strand: chain 'L' and resid 161 through 165 removed outlier: 3.740A pdb=" N GLY L 45 " --> pdb=" O THR L 145 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 118 through 122 Processing sheet with id= AB, first strand: chain 'L' and resid 296 through 298 Processing sheet with id= AC, first strand: chain 'M' and resid 142 through 144 removed outlier: 6.764A pdb=" N LEU M 41 " --> pdb=" O GLY M 143 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE M 161 " --> pdb=" O LEU M 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'M' and resid 118 through 121 removed outlier: 3.862A pdb=" N ILE M 132 " --> pdb=" O ILE M 121 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 161 through 163 removed outlier: 5.727A pdb=" N LEU N 94 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA N 144 " --> pdb=" O LEU N 94 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE N 96 " --> pdb=" O ALA N 144 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 118 through 121 Processing sheet with id= AG, first strand: chain 'N' and resid 295 through 297 1160 hydrogen bonds defined for protein. 3396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 11.29 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 10633 1.36 - 1.51: 8867 1.51 - 1.66: 12407 1.66 - 1.80: 90 1.80 - 1.95: 8 Bond restraints: 32005 Sorted by residual: bond pdb=" O3' DG G 5 " pdb=" P DT G 6 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.50e-02 4.44e+03 8.00e+00 bond pdb=" O3' DG O 5 " pdb=" P DT O 6 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.26e+00 bond pdb=" O3' DA H 14 " pdb=" P DA H 15 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.40e+00 bond pdb=" O3' DG P 11 " pdb=" P DG P 12 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.20e+00 bond pdb=" O3' DT H 13 " pdb=" P DA H 14 " ideal model delta sigma weight residual 1.607 1.577 0.030 1.50e-02 4.44e+03 4.01e+00 ... (remaining 32000 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.07: 1464 106.07 - 113.51: 17832 113.51 - 120.95: 15453 120.95 - 128.39: 8735 128.39 - 135.82: 285 Bond angle restraints: 43769 Sorted by residual: angle pdb=" O3' DC P 8 " pdb=" C3' DC P 8 " pdb=" C2' DC P 8 " ideal model delta sigma weight residual 111.50 105.57 5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" O3' DC H 8 " pdb=" C3' DC H 8 " pdb=" C2' DC H 8 " ideal model delta sigma weight residual 111.50 106.00 5.50 1.50e+00 4.44e-01 1.34e+01 angle pdb=" N GLY D 16 " pdb=" CA GLY D 16 " pdb=" C GLY D 16 " ideal model delta sigma weight residual 113.18 121.41 -8.23 2.37e+00 1.78e-01 1.21e+01 angle pdb=" N GLY C 16 " pdb=" CA GLY C 16 " pdb=" C GLY C 16 " ideal model delta sigma weight residual 113.18 121.32 -8.14 2.37e+00 1.78e-01 1.18e+01 angle pdb=" N GLY A 16 " pdb=" CA GLY A 16 " pdb=" C GLY A 16 " ideal model delta sigma weight residual 113.18 121.27 -8.09 2.37e+00 1.78e-01 1.17e+01 ... (remaining 43764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 18194 32.09 - 64.18: 1108 64.18 - 96.27: 43 96.27 - 128.36: 8 128.36 - 160.45: 6 Dihedral angle restraints: 19359 sinusoidal: 8827 harmonic: 10532 Sorted by residual: dihedral pdb=" O1B ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PB ADP A 400 " pdb=" PA ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 139.55 160.45 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP I 400 " pdb=" O3A ADP I 400 " pdb=" PB ADP I 400 " pdb=" PA ADP I 400 " ideal model delta sinusoidal sigma weight residual 300.00 148.16 151.84 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PA ADP A 400 " pdb=" PB ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 177.84 122.16 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 19356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3388 0.034 - 0.067: 1144 0.067 - 0.101: 330 0.101 - 0.134: 173 0.134 - 0.168: 8 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CA ILE D 290 " pdb=" N ILE D 290 " pdb=" C ILE D 290 " pdb=" CB ILE D 290 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" C3' DC P 8 " pdb=" C4' DC P 8 " pdb=" O3' DC P 8 " pdb=" C2' DC P 8 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILE L 290 " pdb=" N ILE L 290 " pdb=" C ILE L 290 " pdb=" CB ILE L 290 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 5040 not shown) Planarity restraints: 5310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 111 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO L 112 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 112 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 286 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO E 287 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 286 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO M 287 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO M 287 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 287 " 0.031 5.00e-02 4.00e+02 ... (remaining 5307 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 144 2.54 - 3.13: 22048 3.13 - 3.72: 47849 3.72 - 4.31: 67684 4.31 - 4.90: 114249 Nonbonded interactions: 251974 Sorted by model distance: nonbonded pdb=" OD1 ASP I 97 " pdb="MG MG I 401 " model vdw 1.944 2.170 nonbonded pdb=" OD1 ASP A 97 " pdb="MG MG A 401 " model vdw 1.952 2.170 nonbonded pdb=" OE2 GLU A 98 " pdb="MG MG A 401 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP I 97 " pdb="MG MG I 401 " model vdw 2.026 2.170 nonbonded pdb=" OE1 GLU C 98 " pdb="MG MG C 401 " model vdw 2.087 2.170 ... (remaining 251969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'B' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'C' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'D' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'E' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'F' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'I' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'J' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'K' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'L' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'M' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'N' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) } ncs_group { reference = (chain 'G' and resid -1 through 21) selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 3 through 25) selection = chain 'P' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.080 Check model and map are aligned: 0.440 Set scattering table: 0.350 Process input model: 87.850 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.004 0.042 32005 Z= 0.256 Angle : 0.635 9.423 43769 Z= 0.323 Chirality : 0.041 0.168 5043 Planarity : 0.005 0.060 5310 Dihedral : 18.231 160.452 12603 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3653 helix: 1.32 (0.12), residues: 1902 sheet: -0.09 (0.24), residues: 534 loop : -0.05 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE A 44 TYR 0.014 0.001 TYR K 111 ARG 0.006 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8625 (ttt) cc_final: 0.8423 (ttt) REVERT: A 241 ASP cc_start: 0.7917 (m-30) cc_final: 0.7716 (m-30) REVERT: B 35 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8174 (mtmm) REVERT: C 104 ARG cc_start: 0.6952 (tpp80) cc_final: 0.6336 (mmp80) REVERT: D 12 ASP cc_start: 0.8011 (m-30) cc_final: 0.7796 (m-30) REVERT: E 300 ARG cc_start: 0.6519 (ttm-80) cc_final: 0.6315 (mmt90) REVERT: F 114 MET cc_start: 0.9071 (ptp) cc_final: 0.8752 (ptm) REVERT: F 178 MET cc_start: 0.7982 (mtp) cc_final: 0.7766 (mtt) REVERT: J 9 LYS cc_start: 0.7767 (mttp) cc_final: 0.7069 (mmtt) REVERT: J 246 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7897 (mt-10) REVERT: K 250 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7709 (mtm-85) REVERT: L 147 ARG cc_start: 0.7205 (mmm-85) cc_final: 0.6881 (mmm-85) REVERT: N 9 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7991 (mmmt) REVERT: N 89 GLU cc_start: 0.7215 (tt0) cc_final: 0.6959 (mt-10) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.5530 time to fit residues: 327.0178 Evaluate side-chains 298 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 338 optimal weight: 10.0000 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS I 175 GLN I 292 GLN J 219 GLN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32005 Z= 0.298 Angle : 0.632 8.440 43769 Z= 0.308 Chirality : 0.042 0.166 5043 Planarity : 0.005 0.073 5310 Dihedral : 18.176 177.655 5379 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.74 % Allowed : 7.29 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3653 helix: 1.20 (0.12), residues: 1913 sheet: -0.15 (0.24), residues: 515 loop : -0.14 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 100 PHE 0.017 0.001 PHE A 44 TYR 0.016 0.001 TYR K 111 ARG 0.008 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 308 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7988 (mmm) cc_final: 0.7743 (mtp) REVERT: C 104 ARG cc_start: 0.6976 (tpp80) cc_final: 0.6391 (mmp80) REVERT: C 296 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8353 (mtpp) REVERT: E 178 MET cc_start: 0.7796 (mmm) cc_final: 0.7550 (mmm) REVERT: E 282 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8072 (pp20) REVERT: F 114 MET cc_start: 0.9097 (ptp) cc_final: 0.8745 (ptm) REVERT: F 178 MET cc_start: 0.8020 (mtp) cc_final: 0.7812 (mtt) REVERT: J 9 LYS cc_start: 0.7740 (mttp) cc_final: 0.6970 (mmtt) REVERT: J 246 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7939 (mt-10) REVERT: K 250 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8048 (mtm-85) REVERT: L 147 ARG cc_start: 0.7277 (mmm-85) cc_final: 0.7050 (mmm-85) REVERT: L 178 MET cc_start: 0.7728 (mmm) cc_final: 0.7172 (mmm) REVERT: M 32 LYS cc_start: 0.7649 (mttm) cc_final: 0.7196 (mtmm) REVERT: N 89 GLU cc_start: 0.7275 (tt0) cc_final: 0.6919 (mt-10) outliers start: 22 outliers final: 12 residues processed: 320 average time/residue: 0.5762 time to fit residues: 269.3733 Evaluate side-chains 307 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 294 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 79 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 339 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32005 Z= 0.290 Angle : 0.619 9.065 43769 Z= 0.300 Chirality : 0.041 0.159 5043 Planarity : 0.005 0.088 5310 Dihedral : 17.886 161.237 5379 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.97 % Allowed : 10.50 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3653 helix: 1.15 (0.12), residues: 1913 sheet: -0.24 (0.23), residues: 512 loop : -0.27 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 100 PHE 0.016 0.001 PHE A 44 TYR 0.015 0.001 TYR K 111 ARG 0.012 0.000 ARG J 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 312 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7978 (mmm) cc_final: 0.7751 (mtp) REVERT: C 104 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6404 (mmp80) REVERT: D 178 MET cc_start: 0.7567 (mmm) cc_final: 0.7029 (mmm) REVERT: E 178 MET cc_start: 0.7798 (mmm) cc_final: 0.7488 (mmm) REVERT: F 114 MET cc_start: 0.9113 (ptp) cc_final: 0.8797 (ptm) REVERT: F 178 MET cc_start: 0.8094 (mtp) cc_final: 0.7890 (mtt) REVERT: J 9 LYS cc_start: 0.7606 (mttp) cc_final: 0.6890 (mmtt) REVERT: J 178 MET cc_start: 0.7869 (mmt) cc_final: 0.7647 (mmm) REVERT: J 246 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7940 (mt-10) REVERT: K 250 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8084 (mtm-85) REVERT: L 147 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.7111 (mmm-85) REVERT: L 178 MET cc_start: 0.7699 (mmm) cc_final: 0.7172 (mmm) REVERT: M 32 LYS cc_start: 0.7706 (mttm) cc_final: 0.7300 (mtmm) REVERT: N 89 GLU cc_start: 0.7411 (tt0) cc_final: 0.6982 (mt-10) outliers start: 29 outliers final: 17 residues processed: 331 average time/residue: 0.5475 time to fit residues: 267.4263 Evaluate side-chains 314 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 297 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 282 GLU Chi-restraints excluded: chain N residue 79 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 177 optimal weight: 30.0000 chunk 322 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32005 Z= 0.322 Angle : 0.636 8.792 43769 Z= 0.308 Chirality : 0.042 0.205 5043 Planarity : 0.005 0.090 5310 Dihedral : 17.746 170.746 5379 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.47 % Allowed : 12.07 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3653 helix: 1.04 (0.12), residues: 1920 sheet: -0.32 (0.23), residues: 529 loop : -0.31 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 100 PHE 0.017 0.002 PHE A 44 TYR 0.016 0.001 TYR K 111 ARG 0.010 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7965 (mmm) cc_final: 0.7748 (mtp) REVERT: C 104 ARG cc_start: 0.7123 (tpp80) cc_final: 0.6481 (mmp80) REVERT: D 178 MET cc_start: 0.7578 (mmm) cc_final: 0.7152 (mmm) REVERT: E 178 MET cc_start: 0.7692 (mmm) cc_final: 0.7348 (mmm) REVERT: F 114 MET cc_start: 0.9119 (ptp) cc_final: 0.8806 (ptm) REVERT: F 178 MET cc_start: 0.8078 (mtp) cc_final: 0.7870 (mtt) REVERT: F 210 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7780 (mp) REVERT: J 9 LYS cc_start: 0.7621 (mttp) cc_final: 0.6879 (mmtt) REVERT: J 10 THR cc_start: 0.8874 (m) cc_final: 0.8660 (p) REVERT: J 246 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7932 (mt-10) REVERT: L 147 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.7109 (mmm-85) REVERT: L 178 MET cc_start: 0.7805 (mmm) cc_final: 0.7290 (mmm) REVERT: M 32 LYS cc_start: 0.7876 (mttm) cc_final: 0.7490 (mtmm) REVERT: N 89 GLU cc_start: 0.7472 (tt0) cc_final: 0.7020 (mt-10) REVERT: N 187 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7304 (mtp180) outliers start: 44 outliers final: 28 residues processed: 335 average time/residue: 0.5476 time to fit residues: 269.9592 Evaluate side-chains 319 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 290 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 79 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 323 optimal weight: 0.0000 chunk 90 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32005 Z= 0.191 Angle : 0.567 8.563 43769 Z= 0.276 Chirality : 0.039 0.144 5043 Planarity : 0.005 0.073 5310 Dihedral : 17.455 178.985 5379 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.34 % Allowed : 13.38 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3653 helix: 1.26 (0.12), residues: 1916 sheet: -0.32 (0.23), residues: 527 loop : -0.11 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 100 PHE 0.016 0.001 PHE I 44 TYR 0.011 0.001 TYR C 111 ARG 0.011 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 3.885 Fit side-chains revert: symmetry clash REVERT: B 178 MET cc_start: 0.7938 (mmm) cc_final: 0.7721 (mtp) REVERT: C 104 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6379 (mmp80) REVERT: C 296 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8177 (mtpt) REVERT: D 178 MET cc_start: 0.7564 (mmm) cc_final: 0.7119 (mmm) REVERT: F 114 MET cc_start: 0.9141 (ptp) cc_final: 0.8845 (ptm) REVERT: F 178 MET cc_start: 0.7998 (mtp) cc_final: 0.7791 (mtt) REVERT: J 9 LYS cc_start: 0.7584 (mttp) cc_final: 0.6865 (mmtt) REVERT: J 10 THR cc_start: 0.8871 (m) cc_final: 0.8663 (p) REVERT: L 147 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.7084 (mmm-85) REVERT: L 178 MET cc_start: 0.7762 (mmm) cc_final: 0.7281 (mmm) REVERT: M 32 LYS cc_start: 0.7671 (mttm) cc_final: 0.7313 (mtmm) REVERT: N 114 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8646 (mtm) REVERT: N 187 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7294 (mtp180) outliers start: 40 outliers final: 23 residues processed: 336 average time/residue: 0.5379 time to fit residues: 267.0230 Evaluate side-chains 317 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 293 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 360 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32005 Z= 0.215 Angle : 0.580 10.345 43769 Z= 0.280 Chirality : 0.039 0.150 5043 Planarity : 0.005 0.188 5310 Dihedral : 17.342 172.641 5379 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.54 % Allowed : 13.81 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3653 helix: 1.27 (0.12), residues: 1916 sheet: -0.28 (0.23), residues: 531 loop : -0.10 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 100 PHE 0.016 0.001 PHE I 44 TYR 0.012 0.001 TYR C 111 ARG 0.028 0.000 ARG J 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 302 time to evaluate : 3.367 Fit side-chains revert: symmetry clash REVERT: B 178 MET cc_start: 0.7983 (mmm) cc_final: 0.7723 (mtp) REVERT: C 104 ARG cc_start: 0.7103 (tpp80) cc_final: 0.6492 (mmp80) REVERT: C 296 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8172 (mtpt) REVERT: D 178 MET cc_start: 0.7555 (mmm) cc_final: 0.7113 (mmm) REVERT: F 114 MET cc_start: 0.9131 (ptp) cc_final: 0.8812 (ptm) REVERT: F 178 MET cc_start: 0.8076 (mtp) cc_final: 0.7876 (mtt) REVERT: J 9 LYS cc_start: 0.7539 (mttp) cc_final: 0.6802 (mmtt) REVERT: J 10 THR cc_start: 0.8871 (m) cc_final: 0.8664 (p) REVERT: J 190 GLU cc_start: 0.7193 (tp30) cc_final: 0.6883 (tp30) REVERT: L 147 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.7096 (mmm-85) REVERT: L 178 MET cc_start: 0.7785 (mmm) cc_final: 0.7289 (mmm) REVERT: M 32 LYS cc_start: 0.7684 (mttm) cc_final: 0.7342 (mtmm) REVERT: N 114 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8655 (mtm) REVERT: N 187 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7284 (mtp180) outliers start: 46 outliers final: 35 residues processed: 337 average time/residue: 0.5185 time to fit residues: 258.8441 Evaluate side-chains 331 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain I residue 109 HIS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 204 optimal weight: 0.0020 chunk 303 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 359 optimal weight: 3.9990 chunk 224 optimal weight: 0.1980 chunk 219 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 GLN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32005 Z= 0.180 Angle : 0.562 8.126 43769 Z= 0.273 Chirality : 0.039 0.158 5043 Planarity : 0.005 0.175 5310 Dihedral : 17.181 162.061 5379 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.54 % Allowed : 14.25 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3653 helix: 1.35 (0.12), residues: 1904 sheet: -0.26 (0.23), residues: 532 loop : -0.07 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.025 0.001 HIS I 109 PHE 0.015 0.001 PHE I 44 TYR 0.011 0.001 TYR D 111 ARG 0.030 0.000 ARG J 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7973 (mmm) cc_final: 0.7715 (mtp) REVERT: C 28 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7264 (mp) REVERT: C 104 ARG cc_start: 0.7101 (tpp80) cc_final: 0.6491 (mmp80) REVERT: C 296 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8181 (mtpt) REVERT: D 178 MET cc_start: 0.7534 (mmm) cc_final: 0.7104 (mmm) REVERT: E 246 GLU cc_start: 0.7630 (tt0) cc_final: 0.7429 (mt-10) REVERT: F 114 MET cc_start: 0.9126 (ptp) cc_final: 0.8795 (ptm) REVERT: F 178 MET cc_start: 0.7997 (mtp) cc_final: 0.7796 (mtt) REVERT: J 9 LYS cc_start: 0.7525 (mttp) cc_final: 0.6797 (mmtt) REVERT: J 10 THR cc_start: 0.8863 (m) cc_final: 0.8655 (p) REVERT: K 191 GLU cc_start: 0.7806 (mp0) cc_final: 0.7598 (mp0) REVERT: L 147 ARG cc_start: 0.7288 (mmm-85) cc_final: 0.7086 (mmm-85) REVERT: L 178 MET cc_start: 0.7771 (mmm) cc_final: 0.7314 (mmm) REVERT: M 32 LYS cc_start: 0.7712 (mttm) cc_final: 0.7390 (mtmm) REVERT: N 114 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8666 (mtm) REVERT: N 187 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7278 (mtp180) outliers start: 46 outliers final: 36 residues processed: 341 average time/residue: 0.5329 time to fit residues: 269.5222 Evaluate side-chains 337 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 299 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 HIS ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32005 Z= 0.163 Angle : 0.548 7.892 43769 Z= 0.265 Chirality : 0.038 0.141 5043 Planarity : 0.005 0.084 5310 Dihedral : 16.913 147.072 5379 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.51 % Allowed : 14.62 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3653 helix: 1.44 (0.12), residues: 1904 sheet: -0.21 (0.23), residues: 533 loop : -0.00 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 100 PHE 0.015 0.001 PHE I 44 TYR 0.012 0.001 TYR D 111 ARG 0.017 0.000 ARG J 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 317 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7985 (mmm) cc_final: 0.7739 (mtp) REVERT: C 28 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7289 (mp) REVERT: C 104 ARG cc_start: 0.6995 (tpp80) cc_final: 0.6516 (mmp80) REVERT: C 296 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8186 (mtpt) REVERT: D 119 MET cc_start: 0.6825 (ttt) cc_final: 0.6553 (ttt) REVERT: D 178 MET cc_start: 0.7571 (mmm) cc_final: 0.7193 (mmm) REVERT: E 178 MET cc_start: 0.7585 (mmm) cc_final: 0.7372 (mtp) REVERT: E 246 GLU cc_start: 0.7616 (tt0) cc_final: 0.7403 (mt-10) REVERT: E 310 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7536 (mtm-85) REVERT: F 114 MET cc_start: 0.9117 (ptp) cc_final: 0.8774 (ptm) REVERT: F 178 MET cc_start: 0.7995 (mtp) cc_final: 0.7791 (mtt) REVERT: I 109 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8222 (m170) REVERT: J 9 LYS cc_start: 0.7511 (mttp) cc_final: 0.6791 (mmtt) REVERT: J 10 THR cc_start: 0.8858 (m) cc_final: 0.8648 (p) REVERT: L 178 MET cc_start: 0.7784 (mmm) cc_final: 0.7312 (mmm) REVERT: M 32 LYS cc_start: 0.7681 (mttm) cc_final: 0.7375 (mtmm) REVERT: M 307 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.5924 (tt) REVERT: N 114 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8695 (mtm) REVERT: N 187 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7267 (mtp180) outliers start: 45 outliers final: 32 residues processed: 351 average time/residue: 0.5590 time to fit residues: 290.8837 Evaluate side-chains 339 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 303 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain I residue 109 HIS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 307 LEU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 114 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 333 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS D 164 HIS F 60 HIS I 175 GLN ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 HIS ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32005 Z= 0.257 Angle : 0.600 8.603 43769 Z= 0.289 Chirality : 0.040 0.155 5043 Planarity : 0.005 0.141 5310 Dihedral : 17.058 147.038 5379 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.54 % Allowed : 15.02 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3653 helix: 1.24 (0.12), residues: 1907 sheet: -0.32 (0.23), residues: 540 loop : -0.13 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS I 109 PHE 0.015 0.001 PHE A 44 TYR 0.014 0.001 TYR K 111 ARG 0.017 0.000 ARG J 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7979 (mmm) cc_final: 0.7727 (mtp) REVERT: C 28 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7315 (mp) REVERT: C 296 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8199 (mtpt) REVERT: D 178 MET cc_start: 0.7603 (mmm) cc_final: 0.7209 (mmm) REVERT: E 178 MET cc_start: 0.7608 (mmm) cc_final: 0.7367 (mtp) REVERT: E 246 GLU cc_start: 0.7718 (tt0) cc_final: 0.7506 (mt-10) REVERT: F 114 MET cc_start: 0.9104 (ptp) cc_final: 0.8763 (ptm) REVERT: F 178 MET cc_start: 0.8059 (mtp) cc_final: 0.7852 (mtt) REVERT: I 109 HIS cc_start: 0.9178 (OUTLIER) cc_final: 0.8918 (m170) REVERT: J 9 LYS cc_start: 0.7681 (mttp) cc_final: 0.6847 (mmtt) REVERT: L 178 MET cc_start: 0.7783 (mmm) cc_final: 0.7312 (mmm) REVERT: M 32 LYS cc_start: 0.7835 (mttm) cc_final: 0.7526 (mtmm) REVERT: M 307 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6054 (tt) REVERT: N 114 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8702 (mtm) REVERT: N 187 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7270 (mtp180) outliers start: 46 outliers final: 38 residues processed: 328 average time/residue: 0.5502 time to fit residues: 271.1956 Evaluate side-chains 333 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 291 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain I residue 109 HIS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 307 LEU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.9980 chunk 354 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 342 optimal weight: 1.9990 chunk 295 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 228 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS F 285 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 HIS ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32005 Z= 0.167 Angle : 0.559 11.946 43769 Z= 0.269 Chirality : 0.038 0.176 5043 Planarity : 0.005 0.070 5310 Dihedral : 16.778 147.586 5379 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.37 % Allowed : 15.32 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3653 helix: 1.39 (0.12), residues: 1909 sheet: -0.26 (0.23), residues: 523 loop : -0.01 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS K 40 PHE 0.016 0.001 PHE I 44 TYR 0.011 0.001 TYR D 111 ARG 0.014 0.000 ARG C 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 300 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7973 (mmm) cc_final: 0.7719 (mtp) REVERT: C 28 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7292 (mp) REVERT: C 296 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8192 (mtpt) REVERT: D 119 MET cc_start: 0.6824 (ttt) cc_final: 0.6560 (ttt) REVERT: D 178 MET cc_start: 0.7575 (mmm) cc_final: 0.7210 (mmm) REVERT: E 119 MET cc_start: 0.8063 (ptm) cc_final: 0.7658 (ttt) REVERT: E 178 MET cc_start: 0.7580 (mmm) cc_final: 0.7365 (mtp) REVERT: E 246 GLU cc_start: 0.7626 (tt0) cc_final: 0.7425 (mt-10) REVERT: E 310 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7576 (mtm-85) REVERT: F 114 MET cc_start: 0.9118 (ptp) cc_final: 0.8776 (ptm) REVERT: J 9 LYS cc_start: 0.7535 (mttp) cc_final: 0.6717 (mmtt) REVERT: L 178 MET cc_start: 0.7778 (mmm) cc_final: 0.7343 (mmm) REVERT: M 32 LYS cc_start: 0.7737 (mttm) cc_final: 0.7429 (mtmm) REVERT: M 243 LEU cc_start: 0.7483 (mt) cc_final: 0.7232 (mt) REVERT: M 307 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.5982 (tt) REVERT: N 9 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8215 (mmmt) REVERT: N 114 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8706 (mtm) REVERT: N 187 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7262 (mtp180) outliers start: 41 outliers final: 34 residues processed: 331 average time/residue: 0.5587 time to fit residues: 273.9205 Evaluate side-chains 335 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 298 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 307 LEU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 20.0000 chunk 315 optimal weight: 0.2980 chunk 90 optimal weight: 9.9990 chunk 272 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 292 GLN ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.168139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128852 restraints weight = 35476.990| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.12 r_work: 0.3186 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32005 Z= 0.145 Angle : 0.553 11.921 43769 Z= 0.266 Chirality : 0.038 0.214 5043 Planarity : 0.006 0.237 5310 Dihedral : 16.528 147.357 5379 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.20 % Allowed : 15.55 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3653 helix: 1.49 (0.12), residues: 1910 sheet: -0.25 (0.23), residues: 523 loop : 0.10 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS D 100 PHE 0.015 0.001 PHE I 44 TYR 0.011 0.001 TYR D 111 ARG 0.026 0.000 ARG J 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6404.42 seconds wall clock time: 116 minutes 34.19 seconds (6994.19 seconds total)