Starting phenix.real_space_refine on Sun Feb 18 13:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/02_2024/7s65_24850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/02_2024/7s65_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_24850/02_2024/7s65_24850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/02_2024/7s65_24850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/02_2024/7s65_24850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s65_24850/02_2024/7s65_24850_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 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. 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-5238/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, 'ADP': 1, 'ATP': 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, 'ADP': 1, 'ATP': 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: 15.84, per 1000 atoms: 0.72 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: 7.71 Conformation dependent library (CDL) restraints added in 5.8 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: 4.68 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: 7.22 Time building geometry restraints manager: 8.38 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: 13387 30.91 - 61.83: 200 61.83 - 92.74: 26 92.74 - 123.66: 4 123.66 - 154.57: 4 Dihedral angle restraints: 13621 sinusoidal: 5722 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 13618 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 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.960 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 62.370 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.100 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 12.104 154.571 8551 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 % Allowed : 0.86 % Favored : 98.88 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.011 TRP E 92 HIS 0.007 0.003 HIS C 429 PHE 0.054 0.009 PHE F 237 TYR 0.089 0.010 TYR A 235 ARG 0.011 0.002 ARG F 161 *********************** 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 : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7596 (tptt) cc_final: 0.7376 (tttt) REVERT: A 458 MET cc_start: 0.7119 (tpt) cc_final: 0.6658 (tpt) REVERT: B 471 MET cc_start: 0.6373 (mpt) cc_final: 0.5995 (mpp) REVERT: C 172 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7157 (tttt) REVERT: C 420 MET cc_start: 0.4519 (ttm) cc_final: 0.4304 (ttm) REVERT: D 85 LYS cc_start: 0.7780 (tptt) cc_final: 0.7512 (tttt) REVERT: D 193 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7221 (ttt180) REVERT: D 309 LYS cc_start: 0.7636 (mmtm) cc_final: 0.7414 (mppt) REVERT: D 458 MET cc_start: 0.7055 (tpt) cc_final: 0.6592 (tpt) REVERT: E 471 MET cc_start: 0.6337 (mpt) cc_final: 0.6025 (mpp) REVERT: F 172 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7247 (tttt) outliers start: 6 outliers final: 1 residues processed: 628 average time/residue: 0.4084 time to fit residues: 370.3341 Evaluate side-chains 403 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 427 ASP 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 B 15 HIS B 86 ASN C 308 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 203 ASN D 341 GLN D 414 ASN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22425 Z= 0.260 Angle : 0.640 9.621 30315 Z= 0.337 Chirality : 0.045 0.275 3385 Planarity : 0.004 0.051 3868 Dihedral : 11.017 150.059 3401 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.38 % Allowed : 7.78 % Favored : 90.83 % 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: 0.67 (0.15), residues: 2739 helix: 0.61 (0.15), residues: 1027 sheet: 0.91 (0.19), residues: 732 loop : 0.11 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 92 HIS 0.006 0.001 HIS A 423 PHE 0.028 0.002 PHE E 59 TYR 0.013 0.002 TYR C 350 ARG 0.006 0.001 ARG E 216 *********************** 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 476 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 444 time to evaluate : 2.456 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.7402 (mtp) cc_final: 0.7144 (mtp) REVERT: A 323 GLN cc_start: 0.6515 (mm110) cc_final: 0.6256 (mm-40) REVERT: A 458 MET cc_start: 0.6971 (tpt) cc_final: 0.6479 (tpt) REVERT: B 100 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6509 (mt-10) REVERT: B 471 MET cc_start: 0.6085 (mpt) cc_final: 0.5720 (mpp) REVERT: C 32 SER cc_start: 0.8520 (p) cc_final: 0.8171 (p) REVERT: C 170 ARG cc_start: 0.7152 (mmm160) cc_final: 0.6920 (mtp180) REVERT: C 334 ASP cc_start: 0.7489 (t0) cc_final: 0.7216 (t0) REVERT: C 336 GLU cc_start: 0.7921 (tp30) cc_final: 0.7678 (tp30) REVERT: C 448 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6645 (pt0) REVERT: C 475 LYS cc_start: 0.6573 (mmmt) cc_final: 0.6072 (mtpt) REVERT: D 309 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7314 (mppt) REVERT: D 458 MET cc_start: 0.6997 (tpt) cc_final: 0.6496 (tpt) REVERT: E 100 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6516 (mt-10) REVERT: F 24 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5697 (mtm) REVERT: F 32 SER cc_start: 0.8504 (p) cc_final: 0.8158 (p) REVERT: F 334 ASP cc_start: 0.7451 (t0) cc_final: 0.7191 (t0) REVERT: F 336 GLU cc_start: 0.7998 (tp30) cc_final: 0.7732 (tp30) outliers start: 32 outliers final: 22 residues processed: 455 average time/residue: 0.4253 time to fit residues: 284.4307 Evaluate side-chains 383 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 360 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 463 HIS B 15 HIS B 58 GLN B 86 ASN B 423 HIS D 203 ASN D 463 HIS E 58 GLN E 86 ASN E 423 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 22425 Z= 0.459 Angle : 0.733 11.242 30315 Z= 0.379 Chirality : 0.050 0.440 3385 Planarity : 0.005 0.045 3868 Dihedral : 11.831 154.744 3401 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.85 % Allowed : 8.26 % Favored : 88.89 % 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: 0.15 (0.15), residues: 2739 helix: 0.33 (0.16), residues: 1029 sheet: 0.66 (0.18), residues: 722 loop : -0.40 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 92 HIS 0.009 0.002 HIS A 230 PHE 0.035 0.003 PHE D 301 TYR 0.019 0.003 TYR C 350 ARG 0.006 0.001 ARG E 184 *********************** 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 462 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 396 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.6654 (mmt) cc_final: 0.6297 (mmt) REVERT: A 458 MET cc_start: 0.6742 (tpt) cc_final: 0.6069 (tpt) REVERT: B 113 GLU cc_start: 0.4620 (mp0) cc_final: 0.4394 (mp0) REVERT: B 471 MET cc_start: 0.6432 (mpt) cc_final: 0.6167 (mpt) REVERT: C 24 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5807 (mtm) REVERT: C 88 ARG cc_start: 0.7569 (tpt170) cc_final: 0.7369 (tpt90) REVERT: C 448 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6747 (pt0) REVERT: C 475 LYS cc_start: 0.6634 (mmmt) cc_final: 0.6295 (mtpt) REVERT: D 361 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 420 MET cc_start: 0.6467 (mmt) cc_final: 0.6086 (mmt) REVERT: D 458 MET cc_start: 0.6834 (tpt) cc_final: 0.6560 (tpt) REVERT: E 24 MET cc_start: 0.6174 (mtt) cc_final: 0.5897 (mtp) REVERT: E 100 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6370 (mt-10) REVERT: E 113 GLU cc_start: 0.4659 (mp0) cc_final: 0.4423 (mp0) REVERT: E 471 MET cc_start: 0.6199 (mpp) cc_final: 0.5884 (mtm) REVERT: F 88 ARG cc_start: 0.7563 (tpt170) cc_final: 0.7345 (tpt90) REVERT: F 448 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6729 (pt0) REVERT: F 475 LYS cc_start: 0.6827 (mmmt) cc_final: 0.6474 (mtpt) outliers start: 66 outliers final: 49 residues processed: 429 average time/residue: 0.4015 time to fit residues: 251.9499 Evaluate side-chains 405 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 355 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 15 HIS ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 308 ASN D 153 GLN E 86 ASN E 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22425 Z= 0.192 Angle : 0.549 8.578 30315 Z= 0.285 Chirality : 0.043 0.227 3385 Planarity : 0.004 0.051 3868 Dihedral : 11.091 152.995 3401 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.86 % Allowed : 10.42 % Favored : 87.72 % 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: 0.49 (0.15), residues: 2739 helix: 0.77 (0.16), residues: 1015 sheet: 0.63 (0.18), residues: 732 loop : -0.22 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 92 HIS 0.004 0.001 HIS D 423 PHE 0.023 0.002 PHE B 301 TYR 0.010 0.001 TYR B 235 ARG 0.004 0.000 ARG A 257 *********************** 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 439 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 396 time to evaluate : 2.519 Fit side-chains REVERT: B 185 ILE cc_start: 0.8938 (mm) cc_final: 0.8383 (mt) REVERT: C 24 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5608 (mtm) REVERT: C 88 ARG cc_start: 0.7380 (tpt170) cc_final: 0.7121 (tpt90) REVERT: C 336 GLU cc_start: 0.7972 (tp30) cc_final: 0.7767 (tp30) REVERT: C 448 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6668 (pt0) REVERT: C 475 LYS cc_start: 0.6542 (mmmt) cc_final: 0.6273 (mtpt) REVERT: E 100 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6371 (mt-10) REVERT: E 185 ILE cc_start: 0.8888 (mm) cc_final: 0.8329 (mt) REVERT: E 471 MET cc_start: 0.6409 (mpp) cc_final: 0.5916 (mtm) REVERT: F 24 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5598 (mtm) REVERT: F 88 ARG cc_start: 0.7426 (tpt170) cc_final: 0.7172 (tpt90) REVERT: F 336 GLU cc_start: 0.7987 (tp30) cc_final: 0.7785 (tp30) REVERT: F 448 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6630 (pt0) outliers start: 43 outliers final: 37 residues processed: 414 average time/residue: 0.4105 time to fit residues: 248.1503 Evaluate side-chains 399 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 360 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 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: 9.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN B 86 ASN B 245 ASN E 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 22425 Z= 0.447 Angle : 0.696 14.234 30315 Z= 0.358 Chirality : 0.048 0.240 3385 Planarity : 0.005 0.041 3868 Dihedral : 11.330 156.222 3401 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.72 % Allowed : 11.67 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 2739 helix: 0.35 (0.16), residues: 1025 sheet: 0.42 (0.18), residues: 720 loop : -0.71 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 92 HIS 0.007 0.002 HIS D 230 PHE 0.033 0.003 PHE D 301 TYR 0.018 0.002 TYR F 442 ARG 0.006 0.001 ARG E 184 *********************** 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 439 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 376 time to evaluate : 2.288 Fit side-chains REVERT: A 420 MET cc_start: 0.6184 (mmt) cc_final: 0.5830 (mmt) REVERT: B 292 THR cc_start: 0.8305 (p) cc_final: 0.7974 (p) REVERT: B 471 MET cc_start: 0.6370 (mpp) cc_final: 0.5762 (mtm) REVERT: C 18 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7393 (mp) REVERT: C 24 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5476 (mtm) REVERT: C 88 ARG cc_start: 0.7566 (tpt170) cc_final: 0.7348 (tpt90) REVERT: C 336 GLU cc_start: 0.7978 (tp30) cc_final: 0.7771 (tp30) REVERT: C 448 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6693 (pt0) REVERT: D 420 MET cc_start: 0.6263 (mmt) cc_final: 0.5907 (mmt) REVERT: E 471 MET cc_start: 0.6419 (mpp) cc_final: 0.5842 (mtm) REVERT: F 18 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7416 (mp) REVERT: F 88 ARG cc_start: 0.7550 (tpt170) cc_final: 0.7328 (tpt90) REVERT: F 336 GLU cc_start: 0.8027 (tp30) cc_final: 0.7817 (tp30) REVERT: F 433 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8071 (pt) REVERT: F 448 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6690 (pt0) outliers start: 63 outliers final: 53 residues processed: 405 average time/residue: 0.4040 time to fit residues: 241.9029 Evaluate side-chains 409 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 352 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain F residue 439 LEU 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: 30.0000 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 265 optimal weight: 0.0470 chunk 220 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 58 GLN B 86 ASN B 256 GLN C 33 HIS D 203 ASN E 256 GLN E 308 ASN F 33 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3858 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= 0.205 Angle : 0.535 10.337 30315 Z= 0.278 Chirality : 0.043 0.221 3385 Planarity : 0.004 0.052 3868 Dihedral : 10.722 153.697 3401 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.33 % Allowed : 12.75 % Favored : 84.91 % 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: 0.33 (0.16), residues: 2739 helix: 0.79 (0.16), residues: 1017 sheet: 0.50 (0.18), residues: 732 loop : -0.46 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 92 HIS 0.003 0.001 HIS A 423 PHE 0.022 0.002 PHE B 301 TYR 0.012 0.001 TYR F 442 ARG 0.004 0.000 ARG B 468 *********************** 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 433 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 379 time to evaluate : 2.721 Fit side-chains REVERT: A 309 LYS cc_start: 0.7548 (mppt) cc_final: 0.7288 (mmtt) REVERT: A 420 MET cc_start: 0.6145 (mmt) cc_final: 0.5730 (mmt) REVERT: B 136 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7539 (tptp) REVERT: B 185 ILE cc_start: 0.9035 (mm) cc_final: 0.8597 (mt) REVERT: B 471 MET cc_start: 0.6508 (mpp) cc_final: 0.5822 (mtm) REVERT: C 24 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5322 (mtm) REVERT: C 88 ARG cc_start: 0.7503 (tpt170) cc_final: 0.7298 (tpt90) REVERT: C 433 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8112 (pt) REVERT: C 448 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6681 (pt0) REVERT: D 333 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7049 (mtp) REVERT: D 420 MET cc_start: 0.6222 (mmt) cc_final: 0.5928 (mmt) REVERT: E 185 ILE cc_start: 0.9013 (mm) cc_final: 0.8580 (mt) REVERT: E 241 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.5486 (m-30) REVERT: E 471 MET cc_start: 0.6446 (mpp) cc_final: 0.5862 (mtm) REVERT: F 24 MET cc_start: 0.6038 (OUTLIER) cc_final: 0.5393 (mtm) REVERT: F 420 MET cc_start: 0.5615 (mtp) cc_final: 0.5301 (ttm) REVERT: F 448 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6592 (pt0) outliers start: 54 outliers final: 41 residues processed: 403 average time/residue: 0.4122 time to fit residues: 243.7899 Evaluate side-chains 405 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 359 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN B 58 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 22425 Z= 0.385 Angle : 0.636 12.581 30315 Z= 0.329 Chirality : 0.046 0.234 3385 Planarity : 0.005 0.044 3868 Dihedral : 10.949 157.191 3401 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.81 % Allowed : 12.54 % 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: 0.00 (0.15), residues: 2739 helix: 0.55 (0.16), residues: 1021 sheet: 0.42 (0.18), residues: 712 loop : -0.75 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 92 HIS 0.005 0.001 HIS A 230 PHE 0.029 0.003 PHE D 301 TYR 0.015 0.002 TYR F 402 ARG 0.007 0.001 ARG E 321 *********************** 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 437 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 372 time to evaluate : 2.646 Fit side-chains REVERT: A 309 LYS cc_start: 0.7561 (mppt) cc_final: 0.7266 (mmtt) REVERT: B 471 MET cc_start: 0.6439 (mpp) cc_final: 0.5873 (mtm) REVERT: C 24 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5542 (mtm) REVERT: C 433 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8078 (pt) REVERT: C 448 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6720 (pt0) REVERT: D 333 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6944 (mtp) REVERT: D 420 MET cc_start: 0.6291 (mmt) cc_final: 0.5912 (mmt) REVERT: E 241 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.5724 (m-30) REVERT: E 471 MET cc_start: 0.6310 (mpp) cc_final: 0.5740 (mtm) REVERT: F 448 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6708 (pt0) outliers start: 65 outliers final: 55 residues processed: 402 average time/residue: 0.4259 time to fit residues: 253.9657 Evaluate side-chains 420 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 361 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 58 GLN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22425 Z= 0.338 Angle : 0.607 12.000 30315 Z= 0.315 Chirality : 0.045 0.236 3385 Planarity : 0.004 0.053 3868 Dihedral : 10.973 157.605 3401 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.85 % Allowed : 12.75 % Favored : 84.39 % 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: -0.09 (0.15), residues: 2739 helix: 0.47 (0.16), residues: 1029 sheet: 0.41 (0.18), residues: 710 loop : -0.85 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 462 HIS 0.004 0.001 HIS A 423 PHE 0.027 0.002 PHE E 301 TYR 0.014 0.002 TYR C 194 ARG 0.006 0.001 ARG E 321 *********************** 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 441 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 375 time to evaluate : 2.550 Fit side-chains REVERT: A 309 LYS cc_start: 0.7556 (mppt) cc_final: 0.7263 (mmtt) REVERT: A 420 MET cc_start: 0.6045 (mmt) cc_final: 0.5638 (mmt) REVERT: B 471 MET cc_start: 0.6440 (mpp) cc_final: 0.5852 (mtm) REVERT: C 433 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8123 (pt) REVERT: C 448 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6843 (pt0) REVERT: D 333 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7005 (mtp) REVERT: D 420 MET cc_start: 0.6242 (mmt) cc_final: 0.5917 (mmt) REVERT: E 185 ILE cc_start: 0.9027 (mm) cc_final: 0.8600 (mt) REVERT: E 241 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5670 (m-30) REVERT: E 471 MET cc_start: 0.6502 (mpp) cc_final: 0.5824 (mtm) REVERT: F 420 MET cc_start: 0.5832 (mtp) cc_final: 0.5559 (ttm) REVERT: F 448 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6709 (pt0) outliers start: 66 outliers final: 58 residues processed: 404 average time/residue: 0.3945 time to fit residues: 235.1411 Evaluate side-chains 424 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 363 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 252 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 58 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22425 Z= 0.221 Angle : 0.541 10.398 30315 Z= 0.283 Chirality : 0.043 0.215 3385 Planarity : 0.004 0.051 3868 Dihedral : 10.607 157.137 3401 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.33 % Allowed : 13.40 % Favored : 84.26 % 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: 0.22 (0.15), residues: 2739 helix: 0.76 (0.16), residues: 1017 sheet: 0.44 (0.18), residues: 728 loop : -0.61 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 462 HIS 0.003 0.001 HIS A 423 PHE 0.023 0.002 PHE E 301 TYR 0.013 0.001 TYR A 132 ARG 0.006 0.000 ARG E 321 *********************** 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 430 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 376 time to evaluate : 2.269 Fit side-chains REVERT: A 86 ASN cc_start: 0.7738 (m110) cc_final: 0.7308 (m-40) REVERT: A 309 LYS cc_start: 0.7608 (mppt) cc_final: 0.7351 (mmtt) REVERT: A 420 MET cc_start: 0.5836 (mmt) cc_final: 0.5417 (mmt) REVERT: B 471 MET cc_start: 0.6432 (mpp) cc_final: 0.5892 (mtm) REVERT: C 433 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8140 (pt) REVERT: C 448 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6827 (pt0) REVERT: D 333 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6937 (mtp) REVERT: D 420 MET cc_start: 0.6161 (mmt) cc_final: 0.5837 (mmt) REVERT: E 185 ILE cc_start: 0.9068 (mm) cc_final: 0.8655 (mt) REVERT: E 241 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.5667 (m-30) REVERT: E 471 MET cc_start: 0.6497 (mpp) cc_final: 0.5842 (mtm) REVERT: F 420 MET cc_start: 0.5532 (mtp) cc_final: 0.5330 (ttm) REVERT: F 448 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6727 (pt0) outliers start: 54 outliers final: 48 residues processed: 400 average time/residue: 0.3884 time to fit residues: 228.1143 Evaluate side-chains 413 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 362 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 439 LEU 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: 3.9990 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 256 GLN B 58 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 203 ASN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22425 Z= 0.196 Angle : 0.533 9.884 30315 Z= 0.278 Chirality : 0.042 0.200 3385 Planarity : 0.004 0.053 3868 Dihedral : 10.378 157.395 3401 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.20 % Allowed : 13.96 % Favored : 83.83 % 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: 0.33 (0.16), residues: 2739 helix: 0.87 (0.17), residues: 1017 sheet: 0.46 (0.18), residues: 732 loop : -0.53 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 462 HIS 0.003 0.001 HIS D 423 PHE 0.022 0.002 PHE E 301 TYR 0.010 0.001 TYR B 235 ARG 0.006 0.000 ARG B 321 ********************** 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 421 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 370 time to evaluate : 2.622 Fit side-chains REVERT: A 86 ASN cc_start: 0.7739 (m110) cc_final: 0.7310 (m-40) REVERT: A 309 LYS cc_start: 0.7575 (mppt) cc_final: 0.7320 (mmtt) REVERT: A 323 GLN cc_start: 0.6732 (mm110) cc_final: 0.6503 (mm-40) REVERT: A 471 MET cc_start: 0.5229 (mmm) cc_final: 0.5028 (mmm) REVERT: B 471 MET cc_start: 0.6424 (mpp) cc_final: 0.5909 (mtm) REVERT: C 24 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5476 (mtm) REVERT: C 433 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8126 (pt) REVERT: C 448 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6825 (pt0) REVERT: D 333 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6916 (mtp) REVERT: D 420 MET cc_start: 0.6119 (mmt) cc_final: 0.5804 (mmt) REVERT: E 185 ILE cc_start: 0.9072 (mm) cc_final: 0.8651 (mt) REVERT: E 241 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5560 (m-30) REVERT: E 471 MET cc_start: 0.6497 (mpp) cc_final: 0.5861 (mtm) REVERT: F 420 MET cc_start: 0.5571 (mtp) cc_final: 0.5295 (ttm) REVERT: F 433 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8170 (pt) outliers start: 51 outliers final: 43 residues processed: 393 average time/residue: 0.3905 time to fit residues: 228.9440 Evaluate side-chains 411 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 363 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 341 GLN B 58 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120444 restraints weight = 53681.729| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.51 r_work: 0.3136 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22425 Z= 0.322 Angle : 0.604 12.795 30315 Z= 0.312 Chirality : 0.045 0.221 3385 Planarity : 0.004 0.050 3868 Dihedral : 10.512 159.542 3401 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.46 % Allowed : 14.22 % 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: 0.08 (0.15), residues: 2739 helix: 0.64 (0.16), residues: 1027 sheet: 0.37 (0.18), residues: 736 loop : -0.70 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 462 HIS 0.004 0.001 HIS A 230 PHE 0.027 0.002 PHE E 301 TYR 0.026 0.002 TYR F 132 ARG 0.006 0.001 ARG E 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.22 seconds wall clock time: 96 minutes 27.17 seconds (5787.17 seconds total)