Starting phenix.real_space_refine (version: dev) on Wed Apr 6 17:04:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/04_2022/7s65_24850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/04_2022/7s65_24850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/04_2022/7s65_24850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/04_2022/7s65_24850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/04_2022/7s65_24850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/04_2022/7s65_24850_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 339": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 22049 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3667 Chain: "C" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3626 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 451} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3636 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3667 Conformer: "C" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3667 Chain: "F" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3626 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 451} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ATP': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ATP': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 17.56, per 1000 atoms: 0.80 Number of scatterers: 22049 At special positions: 0 Unit cell: (125.35, 118.45, 110.4, 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 88 16.00 P 34 15.00 Mg 12 11.99 O 4253 8.00 N 3854 7.00 C 13808 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.22 Conformation dependent library (CDL) restraints added in 5.0 seconds 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 20 sheets defined 33.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.894A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.025A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 160 through 174 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'B' and resid 28 through 31 No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.896A pdb=" N SER B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 123 through 136 removed outlier: 4.101A pdb=" N ILE B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B 128 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 157 through 174 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.937A pdb=" N GLY B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 405 Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'C' and resid 28 through 31 No H-bonds generated for 'chain 'C' and resid 28 through 31' Processing helix chain 'C' and resid 52 through 66 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.830A pdb=" N SER C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 123 through 136 Processing helix chain 'C' and resid 157 through 174 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 294 through 308 Processing helix chain 'C' and resid 321 through 331 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 356 through 370 Processing helix chain 'C' and resid 389 through 405 Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 52 through 66 removed outlier: 3.893A pdb=" N LEU D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.025A pdb=" N SER D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 197 through 200 No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'D' and resid 294 through 308 Processing helix chain 'D' and resid 321 through 331 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 389 through 405 Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 52 through 65 Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.895A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 123 through 136 removed outlier: 4.101A pdb=" N ILE E 127 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU E 128 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR E 132 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 294 through 308 Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 356 through 370 Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.937A pdb=" N GLY E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'F' and resid 28 through 31 No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 52 through 66 Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.830A pdb=" N SER F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 123 through 136 Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 268 through 273 Processing helix chain 'F' and resid 294 through 308 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 356 through 370 Processing helix chain 'F' and resid 389 through 405 Processing sheet with id= A, first strand: chain 'A' and resid 234 through 236 removed outlier: 8.346A pdb=" N VAL A 205 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 178 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 44 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET A 180 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY A 46 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR A 182 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 450 through 458 removed outlier: 6.330A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 410 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 286 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 412 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY A 288 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN A 414 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 215 through 225 removed outlier: 6.641A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 178 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL B 44 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET B 180 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY B 46 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR B 182 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 448 through 458 removed outlier: 6.343A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY B 410 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA B 286 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 412 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY B 288 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN B 414 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 470 through 473 Processing sheet with id= H, first strand: chain 'C' and resid 234 through 236 removed outlier: 6.576A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 178 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 44 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET C 180 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLY C 46 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR C 182 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= J, first strand: chain 'C' and resid 476 through 479 removed outlier: 4.091A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY C 410 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA C 286 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE C 412 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY C 288 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN C 414 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 234 through 236 removed outlier: 8.346A pdb=" N VAL D 205 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR D 178 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 44 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET D 180 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLY D 46 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR D 182 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= M, first strand: chain 'D' and resid 450 through 458 removed outlier: 6.329A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY D 410 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA D 286 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE D 412 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY D 288 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN D 414 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 215 through 225 removed outlier: 6.642A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR E 178 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL E 44 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET E 180 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY E 46 " --> pdb=" O MET E 180 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR E 182 " --> pdb=" O GLY E 46 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 237 through 240 Processing sheet with id= P, first strand: chain 'E' and resid 448 through 458 removed outlier: 6.342A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY E 410 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA E 286 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE E 412 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY E 288 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN E 414 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 470 through 473 Processing sheet with id= R, first strand: chain 'F' and resid 234 through 236 removed outlier: 6.575A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR F 178 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL F 44 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET F 180 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLY F 46 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR F 182 " --> pdb=" O GLY F 46 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 237 through 240 Processing sheet with id= T, first strand: chain 'F' and resid 476 through 479 removed outlier: 4.091A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY F 410 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA F 286 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE F 412 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY F 288 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN F 414 " --> pdb=" O GLY F 288 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4320 1.32 - 1.45: 5522 1.45 - 1.57: 12373 1.57 - 1.70: 52 1.70 - 1.83: 158 Bond restraints: 22425 Sorted by residual: bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 bond pdb=" C4 ATP B 603 " pdb=" C5 ATP B 603 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP E 603 " pdb=" C5 ATP E 603 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.74e+01 ... (remaining 22420 not shown) Histogram of bond angle deviations from ideal: 92.47 - 101.58: 58 101.58 - 110.69: 7450 110.69 - 119.79: 11662 119.79 - 128.90: 11031 128.90 - 138.01: 114 Bond angle restraints: 30315 Sorted by residual: angle pdb=" PA ATP D 603 " pdb=" O3A ATP D 603 " pdb=" PB ATP D 603 " ideal model delta sigma weight residual 136.83 104.74 32.09 1.00e+00 1.00e+00 1.03e+03 angle pdb=" PA ATP A 603 " pdb=" O3A ATP A 603 " pdb=" PB ATP A 603 " ideal model delta sigma weight residual 136.83 104.75 32.08 1.00e+00 1.00e+00 1.03e+03 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 108.19 31.68 1.00e+00 1.00e+00 1.00e+03 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 108.21 31.66 1.00e+00 1.00e+00 1.00e+03 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 119.19 20.68 1.00e+00 1.00e+00 4.28e+02 ... (remaining 30310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.91: 13107 30.91 - 61.83: 170 61.83 - 92.74: 26 92.74 - 123.66: 4 123.66 - 154.57: 4 Dihedral angle restraints: 13311 sinusoidal: 5412 harmonic: 7899 Sorted by residual: dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 94.57 -154.57 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PA ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 94.56 -154.56 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O1B ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PB ADP A 602 " pdb=" PA ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 86.80 -146.80 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 13308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2495 0.071 - 0.143: 758 0.143 - 0.214: 118 0.214 - 0.286: 4 0.286 - 0.357: 10 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CA GLU B 77 " pdb=" N GLU B 77 " pdb=" C GLU B 77 " pdb=" CB GLU B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA GLU E 77 " pdb=" N GLU E 77 " pdb=" C GLU E 77 " pdb=" CB GLU E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA BTYR E 402 " pdb=" N TYR E 402 " pdb=" C TYR E 402 " pdb=" CB BTYR E 402 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3382 not shown) Planarity restraints: 3868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 235 " 0.089 2.00e-02 2.50e+03 4.88e-02 4.76e+01 pdb=" CG TYR A 235 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 235 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR A 235 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 235 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 235 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 235 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 235 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 235 " -0.089 2.00e-02 2.50e+03 4.85e-02 4.71e+01 pdb=" CG TYR D 235 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 235 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR D 235 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR D 235 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 235 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR D 235 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 235 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 235 " -0.082 2.00e-02 2.50e+03 4.47e-02 4.00e+01 pdb=" CG TYR E 235 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 235 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR E 235 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 235 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR E 235 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 235 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 235 " -0.070 2.00e-02 2.50e+03 ... (remaining 3865 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 14 2.09 - 2.79: 5855 2.79 - 3.49: 29980 3.49 - 4.20: 56455 4.20 - 4.90: 97622 Nonbonded interactions: 189926 Sorted by model distance: nonbonded pdb=" O1G ATP A 603 " pdb="MG MG A 604 " model vdw 1.385 2.170 nonbonded pdb=" O1G ATP D 603 " pdb="MG MG D 604 " model vdw 1.386 2.170 nonbonded pdb=" O GLU D 198 " pdb=" NZ LYS D 224 " model vdw 1.596 2.520 nonbonded pdb=" O GLU A 198 " pdb=" NZ LYS A 224 " model vdw 1.597 2.520 nonbonded pdb=" OG1 THR D 290 " pdb=" O3B ADP D 602 " model vdw 1.641 2.440 ... (remaining 189921 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 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 473 or resid 601 or resid 603 through 604)) selection = (chain 'B' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 444 or resid 449 through 473 or resid 601 or resid 603 throug \ h 604)) selection = (chain 'C' and (resid 15 through 401 or resid 403 through 416 or resid 427 throu \ gh 444 or resid 449 through 473 or resid 601 or resid 603 through 604)) selection = (chain 'D' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 473 or resid 601 or resid 603 through 604)) selection = (chain 'E' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 444 or resid 449 through 473 or resid 601 or resid 603 throug \ h 604)) selection = (chain 'F' and (resid 15 through 401 or resid 403 through 416 or resid 427 throu \ gh 444 or resid 449 through 473 or resid 601 or resid 603 through 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 12 5.21 5 S 88 5.16 5 C 13808 2.51 5 N 3854 2.21 5 O 4253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.860 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.180 Process input model: 66.030 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.014 0.095 22425 Z= 0.931 Angle : 1.457 32.091 30315 Z= 1.071 Chirality : 0.067 0.357 3385 Planarity : 0.010 0.056 3868 Dihedral : 11.661 154.571 8241 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.26 % 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: 0.19 (0.15), residues: 2739 helix: -0.19 (0.14), residues: 1033 sheet: 1.03 (0.20), residues: 710 loop : 0.02 (0.18), residues: 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 622 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 628 average time/residue: 0.3993 time to fit residues: 364.9777 Evaluate side-chains 402 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2011 time to fit residues: 4.1073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 414 ASN A 463 HIS B 15 HIS B 86 ASN B 423 HIS C 308 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 203 ASN D 341 GLN D 414 ASN D 463 HIS ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.119 22425 Z= 0.263 Angle : 0.654 10.099 30315 Z= 0.346 Chirality : 0.045 0.278 3385 Planarity : 0.005 0.112 3868 Dihedral : 8.697 149.844 3089 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2739 helix: 0.63 (0.15), residues: 1025 sheet: 0.90 (0.19), residues: 732 loop : 0.10 (0.19), residues: 982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 449 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 461 average time/residue: 0.3922 time to fit residues: 265.7116 Evaluate side-chains 377 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 354 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2244 time to fit residues: 12.7978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 249 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 323 GLN B 15 HIS B 58 GLN B 86 ASN D 203 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 86 ASN ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.150 22425 Z= 0.304 Angle : 0.623 9.543 30315 Z= 0.325 Chirality : 0.045 0.238 3385 Planarity : 0.005 0.124 3868 Dihedral : 8.681 150.980 3089 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 2739 helix: 0.62 (0.16), residues: 1039 sheet: 0.82 (0.19), residues: 722 loop : -0.17 (0.18), residues: 978 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 376 time to evaluate : 2.655 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 392 average time/residue: 0.4211 time to fit residues: 242.6485 Evaluate side-chains 360 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 338 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2005 time to fit residues: 11.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN B 308 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN E 308 ASN E 423 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 22425 Z= 0.309 Angle : 0.611 9.249 30315 Z= 0.317 Chirality : 0.045 0.245 3385 Planarity : 0.005 0.082 3868 Dihedral : 8.665 150.833 3089 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 2739 helix: 0.68 (0.16), residues: 1017 sheet: 0.59 (0.18), residues: 732 loop : -0.26 (0.18), residues: 990 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 403 time to evaluate : 2.610 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 410 average time/residue: 0.4123 time to fit residues: 248.2666 Evaluate side-chains 381 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 358 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1992 time to fit residues: 12.4843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 0.0010 chunk 226 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 22425 Z= 0.252 Angle : 0.564 10.923 30315 Z= 0.289 Chirality : 0.043 0.221 3385 Planarity : 0.004 0.113 3868 Dihedral : 8.484 151.937 3089 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.91 % 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: 0.44 (0.15), residues: 2739 helix: 0.85 (0.16), residues: 1013 sheet: 0.53 (0.18), residues: 732 loop : -0.32 (0.18), residues: 994 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 375 time to evaluate : 2.592 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 386 average time/residue: 0.4056 time to fit residues: 230.8709 Evaluate side-chains 372 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 357 time to evaluate : 2.741 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2628 time to fit residues: 11.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 10.0000 chunk 238 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.186 22425 Z= 0.333 Angle : 0.615 12.504 30315 Z= 0.320 Chirality : 0.045 0.224 3385 Planarity : 0.005 0.126 3868 Dihedral : 8.520 152.474 3089 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.43 % 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: 0.29 (0.15), residues: 2739 helix: 0.73 (0.16), residues: 1013 sheet: 0.50 (0.18), residues: 730 loop : -0.47 (0.18), residues: 996 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 359 time to evaluate : 2.898 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 359 average time/residue: 0.3975 time to fit residues: 209.6741 Evaluate side-chains 351 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 341 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1898 time to fit residues: 7.0991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 0.1980 chunk 121 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 22425 Z= 0.239 Angle : 0.546 8.115 30315 Z= 0.282 Chirality : 0.043 0.214 3385 Planarity : 0.004 0.104 3868 Dihedral : 8.370 150.973 3089 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2739 helix: 0.89 (0.17), residues: 1011 sheet: 0.52 (0.18), residues: 726 loop : -0.50 (0.18), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 363 time to evaluate : 2.657 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 370 average time/residue: 0.4080 time to fit residues: 223.0110 Evaluate side-chains 359 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 349 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3556 time to fit residues: 9.9058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.099 22425 Z= 0.479 Angle : 0.701 11.753 30315 Z= 0.360 Chirality : 0.048 0.305 3385 Planarity : 0.006 0.130 3868 Dihedral : 8.771 154.503 3089 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.86 % 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: -0.23 (0.15), residues: 2739 helix: 0.33 (0.16), residues: 1025 sheet: 0.32 (0.18), residues: 710 loop : -0.86 (0.18), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 356 time to evaluate : 2.857 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 361 average time/residue: 0.4282 time to fit residues: 227.2525 Evaluate side-chains 359 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 343 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2223 time to fit residues: 10.5462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 252 optimal weight: 0.0670 chunk 148 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 203 ASN B 256 GLN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 22425 Z= 0.169 Angle : 0.527 8.454 30315 Z= 0.271 Chirality : 0.042 0.209 3385 Planarity : 0.004 0.128 3868 Dihedral : 8.400 152.195 3089 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.26 % 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: 0.32 (0.16), residues: 2739 helix: 0.89 (0.17), residues: 1007 sheet: 0.43 (0.18), residues: 726 loop : -0.52 (0.18), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 377 time to evaluate : 2.603 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 381 average time/residue: 0.4021 time to fit residues: 225.0414 Evaluate side-chains 358 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 352 time to evaluate : 2.570 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2048 time to fit residues: 5.9837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 10.0000 chunk 260 optimal weight: 0.0870 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 180 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.956 22425 Z= 0.402 Angle : 0.611 32.704 30315 Z= 0.324 Chirality : 0.042 0.246 3385 Planarity : 0.005 0.177 3868 Dihedral : 8.237 152.192 3089 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2739 helix: 1.04 (0.17), residues: 1009 sheet: 0.47 (0.18), residues: 732 loop : -0.38 (0.19), residues: 998 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 365 time to evaluate : 2.858 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 366 average time/residue: 0.4107 time to fit residues: 220.8419 Evaluate side-chains 353 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 350 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2365 time to fit residues: 5.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.147044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122155 restraints weight = 53027.409| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.55 r_work: 0.3275 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.3221 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work: 0.3187 rms_B_bonded: 2.93 restraints_weight: 0.0625 r_work: 0.3145 rms_B_bonded: 3.53 restraints_weight: 0.0312 r_work: 0.3091 rms_B_bonded: 4.40 restraints_weight: 0.0156 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.710 22425 Z= 0.338 Angle : 0.592 25.580 30315 Z= 0.320 Chirality : 0.043 0.226 3385 Planarity : 0.005 0.179 3868 Dihedral : 8.187 151.554 3089 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2739 helix: 1.04 (0.17), residues: 1007 sheet: 0.51 (0.18), residues: 728 loop : -0.47 (0.19), residues: 1004 =============================================================================== Job complete usr+sys time: 4782.42 seconds wall clock time: 87 minutes 40.21 seconds (5260.21 seconds total)