Starting phenix.real_space_refine on Tue Mar 19 00:38:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfu_27414/03_2024/8dfu_27414_updated.pdb" } resolution = 3.44 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 60 5.16 5 C 15720 2.51 5 N 3180 2.21 5 O 3690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 54": "OD1" <-> "OD2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "I ASP 54": "OD1" <-> "OD2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "L ASP 54": "OD1" <-> "OD2" Residue "M ASP 54": "OD1" <-> "OD2" Residue "N ASP 54": "OD1" <-> "OD2" Residue "O ASP 54": "OD1" <-> "OD2" Residue "P ASP 54": "OD1" <-> "OD2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "R ASP 54": "OD1" <-> "OD2" Residue "S ASP 54": "OD1" <-> "OD2" Residue "T ASP 54": "OD1" <-> "OD2" Residue "U ASP 54": "OD1" <-> "OD2" Residue "V ASP 54": "OD1" <-> "OD2" Residue "W ASP 54": "OD1" <-> "OD2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "Y ASP 54": "OD1" <-> "OD2" Residue "Z ASP 54": "OD1" <-> "OD2" Residue "0 ASP 54": "OD1" <-> "OD2" Residue "1 ASP 54": "OD1" <-> "OD2" Residue "2 ASP 54": "OD1" <-> "OD2" Residue "3 ASP 54": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22710 Number of models: 1 Model: "" Number of chains: 56 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "A" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "D" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "E" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "F" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "G" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "J" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "K" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "L" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "M" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "N" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "O" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "P" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Q" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "R" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "S" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "T" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "V" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "W" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "X" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Y" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Z" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "0" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "1" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "2" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "3" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'RHR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'RHR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'RHR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'RHR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'RHR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'RHR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.41, per 1000 atoms: 0.50 Number of scatterers: 22710 At special positions: 0 Unit cell: (101.52, 101.52, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 60 15.00 O 3690 8.00 N 3180 7.00 C 15720 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=81, symmetry=0 Number of additional bonds: simple=81, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.79 Conformation dependent library (CDL) restraints added in 3.8 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'B' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY B 36 " --> pdb=" O TRP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY G 36 " --> pdb=" O TRP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA G 70 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY H 36 " --> pdb=" O TRP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA H 70 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY I 36 " --> pdb=" O TRP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY J 36 " --> pdb=" O TRP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY K 36 " --> pdb=" O TRP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA K 70 " --> pdb=" O THR K 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY L 36 " --> pdb=" O TRP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA L 70 " --> pdb=" O THR L 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY M 36 " --> pdb=" O TRP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA M 63 " --> pdb=" O ALA M 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY N 36 " --> pdb=" O TRP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU N 64 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA N 70 " --> pdb=" O THR N 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY O 36 " --> pdb=" O TRP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA O 70 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY P 36 " --> pdb=" O TRP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU P 64 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA P 70 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY Q 36 " --> pdb=" O TRP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Q 70 " --> pdb=" O THR Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA R 63 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY S 36 " --> pdb=" O TRP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA S 63 " --> pdb=" O ALA S 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU S 64 " --> pdb=" O LEU S 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA S 70 " --> pdb=" O THR S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 36 removed outlier: 3.595A pdb=" N GLY T 36 " --> pdb=" O TRP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA T 63 " --> pdb=" O ALA T 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU T 64 " --> pdb=" O LEU T 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA T 70 " --> pdb=" O THR T 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY U 36 " --> pdb=" O TRP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA U 63 " --> pdb=" O ALA U 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA U 70 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY V 36 " --> pdb=" O TRP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA V 63 " --> pdb=" O ALA V 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU V 64 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA V 70 " --> pdb=" O THR V 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY W 36 " --> pdb=" O TRP W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU W 64 " --> pdb=" O LEU W 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA W 70 " --> pdb=" O THR W 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY X 36 " --> pdb=" O TRP X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 83 removed outlier: 4.695A pdb=" N ALA X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU X 64 " --> pdb=" O LEU X 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA X 70 " --> pdb=" O THR X 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 36 removed outlier: 3.597A pdb=" N GLY Y 36 " --> pdb=" O TRP Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU Y 64 " --> pdb=" O LEU Y 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Y 70 " --> pdb=" O THR Y 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY Z 36 " --> pdb=" O TRP Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Z 64 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Z 70 " --> pdb=" O THR Z 66 " (cutoff:3.500A) Processing helix chain '0' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY 0 36 " --> pdb=" O TRP 0 32 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA 0 63 " --> pdb=" O ALA 0 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 0 64 " --> pdb=" O LEU 0 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA 0 70 " --> pdb=" O THR 0 66 " (cutoff:3.500A) Processing helix chain '1' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY 1 36 " --> pdb=" O TRP 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA 1 63 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 1 64 " --> pdb=" O LEU 1 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA 1 70 " --> pdb=" O THR 1 66 " (cutoff:3.500A) Processing helix chain '2' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY 2 36 " --> pdb=" O TRP 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA 2 63 " --> pdb=" O ALA 2 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 2 64 " --> pdb=" O LEU 2 60 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA 2 70 " --> pdb=" O THR 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 36 removed outlier: 3.596A pdb=" N GLY 3 36 " --> pdb=" O TRP 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 83 removed outlier: 4.694A pdb=" N ALA 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 3 64 " --> pdb=" O LEU 3 60 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA 3 70 " --> pdb=" O THR 3 66 " (cutoff:3.500A) 1860 hydrogen bonds defined for protein. 5580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.26 Time building geometry restraints manager: 9.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5910 1.34 - 1.45: 2807 1.45 - 1.57: 14143 1.57 - 1.68: 60 1.68 - 1.80: 120 Bond restraints: 23040 Sorted by residual: bond pdb=" C40 RHR G 201 " pdb=" C41 RHR G 201 " ideal model delta sigma weight residual 1.520 1.558 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C40 RHR A 102 " pdb=" C41 RHR A 102 " ideal model delta sigma weight residual 1.520 1.557 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C40 RHR B 201 " pdb=" C41 RHR B 201 " ideal model delta sigma weight residual 1.520 1.557 -0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" C40 RHR L 201 " pdb=" C41 RHR L 201 " ideal model delta sigma weight residual 1.520 1.557 -0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" C40 RHR H 201 " pdb=" C41 RHR H 201 " ideal model delta sigma weight residual 1.520 1.557 -0.037 2.00e-02 2.50e+03 3.47e+00 ... (remaining 23035 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.35: 632 107.35 - 114.02: 16225 114.02 - 120.69: 8584 120.69 - 127.37: 5219 127.37 - 134.04: 330 Bond angle restraints: 30990 Sorted by residual: angle pdb=" CA GLY Y 65 " pdb=" C GLY Y 65 " pdb=" N THR Y 66 " ideal model delta sigma weight residual 117.13 114.66 2.47 1.03e+00 9.43e-01 5.75e+00 angle pdb=" CA GLY C 65 " pdb=" C GLY C 65 " pdb=" N THR C 66 " ideal model delta sigma weight residual 117.13 114.68 2.45 1.03e+00 9.43e-01 5.68e+00 angle pdb=" CA GLY V 65 " pdb=" C GLY V 65 " pdb=" N THR V 66 " ideal model delta sigma weight residual 117.13 114.68 2.45 1.03e+00 9.43e-01 5.68e+00 angle pdb=" CA GLY U 65 " pdb=" C GLY U 65 " pdb=" N THR U 66 " ideal model delta sigma weight residual 117.13 114.69 2.44 1.03e+00 9.43e-01 5.59e+00 angle pdb=" CA GLY G 65 " pdb=" C GLY G 65 " pdb=" N THR G 66 " ideal model delta sigma weight residual 117.13 114.70 2.43 1.03e+00 9.43e-01 5.56e+00 ... (remaining 30985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 12060 34.63 - 69.25: 1110 69.25 - 103.88: 270 103.88 - 138.50: 60 138.50 - 173.13: 90 Dihedral angle restraints: 13590 sinusoidal: 6480 harmonic: 7110 Sorted by residual: dihedral pdb=" C23 RHR P 201 " pdb=" C24 RHR P 201 " pdb=" C25 RHR P 201 " pdb=" C26 RHR P 201 " ideal model delta sinusoidal sigma weight residual 109.85 -77.02 -173.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 RHR C 201 " pdb=" C24 RHR C 201 " pdb=" C25 RHR C 201 " pdb=" C26 RHR C 201 " ideal model delta sinusoidal sigma weight residual 109.85 -77.06 -173.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 RHR Z 201 " pdb=" C24 RHR Z 201 " pdb=" C25 RHR Z 201 " pdb=" C26 RHR Z 201 " ideal model delta sinusoidal sigma weight residual 109.85 -77.06 -173.09 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.104: 3690 1.104 - 2.208: 0 2.208 - 3.312: 0 3.312 - 4.417: 0 4.417 - 5.521: 180 Chirality restraints: 3870 Sorted by residual: chirality pdb=" C25 RHR A 101 " pdb=" C24 RHR A 101 " pdb=" C26 RHR A 101 " pdb=" C27 RHR A 101 " both_signs ideal model delta sigma weight residual False -2.77 2.76 -5.52 2.00e-01 2.50e+01 7.62e+02 chirality pdb=" C25 RHR Q 202 " pdb=" C24 RHR Q 202 " pdb=" C26 RHR Q 202 " pdb=" C27 RHR Q 202 " both_signs ideal model delta sigma weight residual False -2.77 2.75 -5.52 2.00e-01 2.50e+01 7.62e+02 chirality pdb=" C25 RHR L 202 " pdb=" C24 RHR L 202 " pdb=" C26 RHR L 202 " pdb=" C27 RHR L 202 " both_signs ideal model delta sigma weight residual False -2.77 2.75 -5.52 2.00e-01 2.50e+01 7.61e+02 ... (remaining 3867 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 69 " 0.011 2.00e-02 2.50e+03 8.49e-03 1.26e+00 pdb=" CG PHE R 69 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE R 69 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE R 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 69 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 69 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 69 " -0.011 2.00e-02 2.50e+03 8.48e-03 1.26e+00 pdb=" CG PHE 3 69 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 69 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 3 69 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 69 " 0.011 2.00e-02 2.50e+03 8.47e-03 1.26e+00 pdb=" CG PHE O 69 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE O 69 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE O 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE O 69 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE O 69 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE O 69 " 0.003 2.00e-02 2.50e+03 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 9920 2.95 - 3.44: 22831 3.44 - 3.92: 35730 3.92 - 4.41: 40229 4.41 - 4.90: 63139 Nonbonded interactions: 171849 Sorted by model distance: nonbonded pdb=" N ASP F 4 " pdb=" OD1 ASP F 4 " model vdw 2.461 2.520 nonbonded pdb=" N ASP A 4 " pdb=" OD1 ASP A 4 " model vdw 2.461 2.520 nonbonded pdb=" N ASP S 4 " pdb=" OD1 ASP S 4 " model vdw 2.462 2.520 nonbonded pdb=" N ASP J 4 " pdb=" OD1 ASP J 4 " model vdw 2.462 2.520 nonbonded pdb=" N ASP 0 4 " pdb=" OD1 ASP 0 4 " model vdw 2.462 2.520 ... (remaining 171844 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = (chain 'A' and resid 2 through 85) selection = (chain 'B' and resid 2 through 85) selection = (chain 'C' and resid 2 through 85) selection = (chain 'D' and resid 2 through 85) selection = (chain 'E' and resid 2 through 85) selection = (chain 'F' and resid 2 through 85) selection = (chain 'G' and resid 2 through 85) selection = (chain 'H' and resid 2 through 85) selection = (chain 'I' and resid 2 through 85) selection = (chain 'J' and resid 2 through 85) selection = (chain 'K' and resid 2 through 85) selection = (chain 'L' and resid 2 through 85) selection = (chain 'M' and resid 2 through 85) selection = (chain 'N' and resid 2 through 85) selection = (chain 'O' and resid 2 through 85) selection = (chain 'P' and resid 2 through 85) selection = (chain 'Q' and resid 2 through 85) selection = (chain 'R' and resid 2 through 85) selection = (chain 'S' and resid 2 through 85) selection = (chain 'T' and resid 2 through 85) selection = (chain 'U' and resid 2 through 85) selection = (chain 'V' and resid 2 through 85) selection = (chain 'W' and resid 2 through 85) selection = (chain 'X' and resid 2 through 85) selection = (chain 'Y' and resid 2 through 85) selection = (chain 'Z' and resid 2 through 85) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.790 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 56.500 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.180 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.010 0.038 23040 Z= 0.622 Angle : 0.916 4.275 30990 Z= 0.414 Chirality : 1.184 5.521 3870 Planarity : 0.004 0.025 3150 Dihedral : 31.931 173.128 8970 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2460 helix: 0.84 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 0.06 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 0 28 PHE 0.019 0.003 PHE R 69 ARG 0.001 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8014 (tt0) cc_final: 0.7518 (tt0) REVERT: A 53 GLU cc_start: 0.7695 (tt0) cc_final: 0.7482 (tt0) REVERT: A 54 ASP cc_start: 0.8369 (m-30) cc_final: 0.7990 (m-30) REVERT: A 81 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8388 (tm-30) REVERT: C 81 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 53 GLU cc_start: 0.7935 (tt0) cc_final: 0.7408 (tt0) REVERT: D 81 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 35 ARG cc_start: 0.9001 (ttt90) cc_final: 0.8795 (mtp180) REVERT: E 53 GLU cc_start: 0.7956 (tt0) cc_final: 0.7646 (tt0) REVERT: F 53 GLU cc_start: 0.7869 (tt0) cc_final: 0.7443 (tt0) REVERT: H 81 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8423 (tm-30) REVERT: I 7 GLN cc_start: 0.8305 (tp40) cc_final: 0.7634 (tp40) REVERT: I 11 ASP cc_start: 0.8669 (m-30) cc_final: 0.8143 (m-30) REVERT: I 53 GLU cc_start: 0.7914 (tt0) cc_final: 0.7406 (tt0) REVERT: I 81 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8375 (tm-30) REVERT: J 53 GLU cc_start: 0.7871 (tt0) cc_final: 0.7644 (tt0) REVERT: K 53 GLU cc_start: 0.7964 (tt0) cc_final: 0.7527 (tt0) REVERT: K 81 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8475 (tm-30) REVERT: L 53 GLU cc_start: 0.7906 (tt0) cc_final: 0.7386 (tt0) REVERT: M 53 GLU cc_start: 0.7943 (tt0) cc_final: 0.7419 (tt0) REVERT: N 53 GLU cc_start: 0.7740 (tt0) cc_final: 0.7210 (tt0) REVERT: N 81 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8487 (tm-30) REVERT: P 53 GLU cc_start: 0.7838 (tt0) cc_final: 0.7575 (tt0) REVERT: P 81 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8491 (tm-30) REVERT: Q 7 GLN cc_start: 0.8222 (tp40) cc_final: 0.7830 (tp40) REVERT: Q 11 ASP cc_start: 0.8783 (m-30) cc_final: 0.8502 (m-30) REVERT: Q 53 GLU cc_start: 0.8037 (tt0) cc_final: 0.7619 (tt0) REVERT: R 53 GLU cc_start: 0.7947 (tt0) cc_final: 0.7531 (tt0) REVERT: S 53 GLU cc_start: 0.7889 (tt0) cc_final: 0.7501 (tt0) REVERT: S 81 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8444 (tm-30) REVERT: T 7 GLN cc_start: 0.8268 (tp40) cc_final: 0.7769 (tp40) REVERT: T 11 ASP cc_start: 0.8515 (m-30) cc_final: 0.8167 (m-30) REVERT: T 53 GLU cc_start: 0.7896 (tt0) cc_final: 0.7455 (tt0) REVERT: T 81 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8362 (tm-30) REVERT: U 53 GLU cc_start: 0.7753 (tt0) cc_final: 0.7484 (tt0) REVERT: U 81 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8417 (tm-30) REVERT: V 53 GLU cc_start: 0.7930 (tt0) cc_final: 0.7621 (tt0) REVERT: V 81 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8391 (tm-30) REVERT: W 53 GLU cc_start: 0.7842 (tt0) cc_final: 0.7377 (tt0) REVERT: X 81 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8531 (tm-30) REVERT: Y 53 GLU cc_start: 0.7868 (tt0) cc_final: 0.7391 (tt0) REVERT: Z 53 GLU cc_start: 0.8028 (tt0) cc_final: 0.7657 (tt0) REVERT: 0 35 ARG cc_start: 0.9028 (ttt90) cc_final: 0.8817 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7849 (tt0) cc_final: 0.7603 (tt0) REVERT: 0 74 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7796 (ttp-170) REVERT: 0 81 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8456 (tm-30) REVERT: 1 53 GLU cc_start: 0.7852 (tt0) cc_final: 0.7411 (tt0) REVERT: 1 74 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7836 (ttp-170) REVERT: 1 81 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8450 (tm-30) REVERT: 2 53 GLU cc_start: 0.7707 (tt0) cc_final: 0.7450 (tt0) REVERT: 2 74 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7740 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8384 (tm-30) REVERT: 3 37 SER cc_start: 0.9256 (m) cc_final: 0.9017 (m) REVERT: 3 74 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7741 (ttp-170) REVERT: 3 81 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8474 (tm-30) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.4819 time to fit residues: 279.2368 Evaluate side-chains 346 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23040 Z= 0.163 Angle : 0.506 4.471 30990 Z= 0.246 Chirality : 0.034 0.113 3870 Planarity : 0.004 0.029 3150 Dihedral : 38.134 178.423 4950 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.75 % Allowed : 13.28 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.17), residues: 2460 helix: 2.17 (0.11), residues: 2340 sheet: None (None), residues: 0 loop : 1.03 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 28 PHE 0.006 0.001 PHE C 69 ARG 0.005 0.001 ARG Z 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 412 time to evaluate : 2.159 Fit side-chains REVERT: A 54 ASP cc_start: 0.8295 (m-30) cc_final: 0.7938 (m-30) REVERT: D 11 ASP cc_start: 0.8555 (m-30) cc_final: 0.8080 (m-30) REVERT: D 53 GLU cc_start: 0.7682 (tt0) cc_final: 0.7230 (tt0) REVERT: E 81 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8512 (tm-30) REVERT: F 53 GLU cc_start: 0.7745 (tt0) cc_final: 0.7363 (tt0) REVERT: G 53 GLU cc_start: 0.7467 (tt0) cc_final: 0.7097 (tt0) REVERT: H 81 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8493 (tm-30) REVERT: I 53 GLU cc_start: 0.7669 (tt0) cc_final: 0.7259 (tt0) REVERT: I 81 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8414 (tm-30) REVERT: J 53 GLU cc_start: 0.7685 (tt0) cc_final: 0.7432 (tt0) REVERT: K 53 GLU cc_start: 0.7862 (tt0) cc_final: 0.7442 (tt0) REVERT: M 53 GLU cc_start: 0.7793 (tt0) cc_final: 0.7467 (tt0) REVERT: N 46 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7857 (mtp-110) REVERT: N 81 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8479 (tm-30) REVERT: P 81 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8509 (tm-30) REVERT: Q 53 GLU cc_start: 0.7755 (tt0) cc_final: 0.7376 (tt0) REVERT: S 42 SER cc_start: 0.9124 (p) cc_final: 0.8893 (t) REVERT: S 53 GLU cc_start: 0.7808 (tt0) cc_final: 0.7447 (tt0) REVERT: T 53 GLU cc_start: 0.7771 (tt0) cc_final: 0.7344 (tt0) REVERT: U 53 GLU cc_start: 0.7600 (tt0) cc_final: 0.7337 (tt0) REVERT: U 81 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8515 (tm-30) REVERT: V 11 ASP cc_start: 0.8514 (m-30) cc_final: 0.8288 (m-30) REVERT: V 53 GLU cc_start: 0.7726 (tt0) cc_final: 0.7365 (tt0) REVERT: V 81 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8306 (tm-30) REVERT: W 53 GLU cc_start: 0.7671 (tt0) cc_final: 0.7163 (tt0) REVERT: X 81 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8523 (tm-30) REVERT: Y 53 GLU cc_start: 0.7788 (tt0) cc_final: 0.7320 (tt0) REVERT: 0 35 ARG cc_start: 0.8980 (ttt90) cc_final: 0.8705 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7695 (tt0) cc_final: 0.7484 (tt0) REVERT: 0 74 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7718 (ttp-170) REVERT: 1 53 GLU cc_start: 0.7638 (tt0) cc_final: 0.7205 (tt0) REVERT: 1 74 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7776 (ttp80) REVERT: 1 81 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8483 (tm-30) REVERT: 2 53 GLU cc_start: 0.7590 (tt0) cc_final: 0.7308 (tt0) REVERT: 2 74 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7795 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8402 (tm-30) REVERT: 3 74 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7685 (ttp-170) REVERT: 3 81 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8398 (tm-30) outliers start: 15 outliers final: 10 residues processed: 415 average time/residue: 0.3127 time to fit residues: 205.6926 Evaluate side-chains 367 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 357 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain 3 residue 8 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 23040 Z= 0.315 Angle : 0.609 6.271 30990 Z= 0.295 Chirality : 0.036 0.112 3870 Planarity : 0.004 0.031 3150 Dihedral : 37.784 177.869 4950 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 15.97 % Favored : 81.69 % 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: 3.71 (0.16), residues: 2460 helix: 2.48 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 1.77 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 28 PHE 0.020 0.003 PHE V 69 ARG 0.008 0.001 ARG O 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 366 time to evaluate : 2.155 Fit side-chains REVERT: B 53 GLU cc_start: 0.7910 (tt0) cc_final: 0.7352 (tt0) REVERT: A 46 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7858 (mtm110) REVERT: A 54 ASP cc_start: 0.8401 (m-30) cc_final: 0.8061 (m-30) REVERT: C 81 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8337 (tm-30) REVERT: D 53 GLU cc_start: 0.7776 (tt0) cc_final: 0.7289 (tt0) REVERT: F 53 GLU cc_start: 0.7833 (tt0) cc_final: 0.7344 (tt0) REVERT: G 53 GLU cc_start: 0.7575 (tt0) cc_final: 0.7195 (tt0) REVERT: H 81 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8465 (tm-30) REVERT: I 11 ASP cc_start: 0.8739 (m-30) cc_final: 0.8308 (m-30) REVERT: I 53 GLU cc_start: 0.7851 (tt0) cc_final: 0.7251 (tt0) REVERT: I 81 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8419 (tm-30) REVERT: J 53 GLU cc_start: 0.7850 (tt0) cc_final: 0.7610 (tt0) REVERT: K 53 GLU cc_start: 0.7821 (tt0) cc_final: 0.7339 (tt0) REVERT: L 53 GLU cc_start: 0.7807 (tt0) cc_final: 0.7271 (tt0) REVERT: M 53 GLU cc_start: 0.7826 (tt0) cc_final: 0.7598 (tt0) REVERT: N 7 GLN cc_start: 0.8322 (tp40) cc_final: 0.8009 (tp40) REVERT: N 11 ASP cc_start: 0.8533 (m-30) cc_final: 0.8219 (m-30) REVERT: N 46 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7842 (mtp-110) REVERT: N 53 GLU cc_start: 0.7644 (tt0) cc_final: 0.7138 (tt0) REVERT: N 81 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8520 (tm-30) REVERT: P 81 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8411 (tm-30) REVERT: Q 7 GLN cc_start: 0.8185 (tp40) cc_final: 0.7702 (tp40) REVERT: Q 11 ASP cc_start: 0.8792 (m-30) cc_final: 0.8509 (m-30) REVERT: Q 53 GLU cc_start: 0.7866 (tt0) cc_final: 0.7443 (tt0) REVERT: R 53 GLU cc_start: 0.7835 (tt0) cc_final: 0.7348 (tt0) REVERT: S 53 GLU cc_start: 0.7798 (tt0) cc_final: 0.7384 (tt0) REVERT: T 7 GLN cc_start: 0.8238 (tp40) cc_final: 0.7538 (tp40) REVERT: T 11 ASP cc_start: 0.8566 (m-30) cc_final: 0.8210 (m-30) REVERT: T 53 GLU cc_start: 0.7765 (tt0) cc_final: 0.7335 (tt0) REVERT: U 46 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7940 (mtm110) REVERT: U 81 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8499 (tm-30) REVERT: V 53 GLU cc_start: 0.7814 (tt0) cc_final: 0.7442 (tt0) REVERT: V 81 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8305 (tm-30) REVERT: W 53 GLU cc_start: 0.7761 (tt0) cc_final: 0.7267 (tt0) REVERT: X 81 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8520 (tm-30) REVERT: Y 53 GLU cc_start: 0.7803 (tt0) cc_final: 0.7261 (tt0) REVERT: Z 53 GLU cc_start: 0.7936 (tt0) cc_final: 0.7366 (tt0) REVERT: 0 35 ARG cc_start: 0.9045 (ttt90) cc_final: 0.8801 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7776 (tt0) cc_final: 0.7477 (tt0) REVERT: 0 74 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7758 (ttp-170) REVERT: 0 81 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8403 (tm-30) REVERT: 1 53 GLU cc_start: 0.7763 (tt0) cc_final: 0.7280 (tt0) REVERT: 1 74 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7844 (ttp-170) REVERT: 1 81 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8407 (tm-30) REVERT: 2 53 GLU cc_start: 0.7773 (tt0) cc_final: 0.7328 (tt0) REVERT: 2 74 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7778 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8405 (tm-30) REVERT: 3 74 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7683 (ttp-170) REVERT: 3 81 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8475 (tm-30) outliers start: 47 outliers final: 42 residues processed: 389 average time/residue: 0.3718 time to fit residues: 213.7687 Evaluate side-chains 390 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 348 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 8 MET Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Z residue 78 ILE Chi-restraints excluded: chain 0 residue 78 ILE Chi-restraints excluded: chain 1 residue 80 ASN Chi-restraints excluded: chain 2 residue 78 ILE Chi-restraints excluded: chain 3 residue 8 MET Chi-restraints excluded: chain 3 residue 78 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23040 Z= 0.162 Angle : 0.472 7.001 30990 Z= 0.241 Chirality : 0.032 0.133 3870 Planarity : 0.004 0.035 3150 Dihedral : 36.484 178.805 4950 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.09 % Allowed : 16.82 % Favored : 81.09 % 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: 4.31 (0.17), residues: 2460 helix: 2.86 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.13 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 28 PHE 0.006 0.001 PHE C 69 ARG 0.009 0.001 ARG Q 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 385 time to evaluate : 2.350 Fit side-chains REVERT: A 54 ASP cc_start: 0.8270 (m-30) cc_final: 0.7875 (m-30) REVERT: C 81 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 8 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7757 (ptp) REVERT: D 53 GLU cc_start: 0.7647 (tt0) cc_final: 0.7177 (tt0) REVERT: D 80 ASN cc_start: 0.9021 (t0) cc_final: 0.8817 (t0) REVERT: E 81 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8631 (tm-30) REVERT: F 53 GLU cc_start: 0.7736 (tt0) cc_final: 0.7316 (tt0) REVERT: H 81 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8465 (tm-30) REVERT: I 53 GLU cc_start: 0.7662 (tt0) cc_final: 0.7143 (tt0) REVERT: J 53 GLU cc_start: 0.7679 (tt0) cc_final: 0.7420 (tt0) REVERT: K 53 GLU cc_start: 0.7832 (tt0) cc_final: 0.7367 (tt0) REVERT: M 53 GLU cc_start: 0.7700 (tt0) cc_final: 0.7439 (tt0) REVERT: N 81 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8486 (tm-30) REVERT: P 81 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8397 (tm-30) REVERT: Q 53 GLU cc_start: 0.7679 (tt0) cc_final: 0.7310 (tt0) REVERT: S 53 GLU cc_start: 0.7691 (tt0) cc_final: 0.7337 (tt0) REVERT: U 81 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8448 (tm-30) REVERT: V 53 GLU cc_start: 0.7746 (tt0) cc_final: 0.7351 (tt0) REVERT: V 81 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8244 (tm-30) REVERT: W 53 GLU cc_start: 0.7612 (tt0) cc_final: 0.7101 (tt0) REVERT: X 81 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8459 (tm-30) REVERT: Y 53 GLU cc_start: 0.7778 (tt0) cc_final: 0.7270 (tt0) REVERT: 0 35 ARG cc_start: 0.9038 (ttt90) cc_final: 0.8720 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7683 (tt0) cc_final: 0.7393 (tt0) REVERT: 0 74 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7655 (ttp-170) REVERT: 1 74 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.7806 (ttp80) REVERT: 1 81 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8287 (tm-30) REVERT: 2 53 GLU cc_start: 0.7617 (tt0) cc_final: 0.7142 (tt0) REVERT: 2 74 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7781 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8365 (tm-30) REVERT: 3 74 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7610 (ttp80) REVERT: 3 81 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8374 (tm-30) outliers start: 42 outliers final: 8 residues processed: 417 average time/residue: 0.2878 time to fit residues: 198.1350 Evaluate side-chains 357 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 348 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23040 Z= 0.230 Angle : 0.511 7.309 30990 Z= 0.265 Chirality : 0.036 0.243 3870 Planarity : 0.004 0.032 3150 Dihedral : 36.752 179.896 4950 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.49 % Allowed : 17.46 % Favored : 80.05 % 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: 4.35 (0.17), residues: 2460 helix: 2.87 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.37 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 28 PHE 0.014 0.001 PHE C 69 ARG 0.007 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 357 time to evaluate : 2.332 Fit side-chains REVERT: A 54 ASP cc_start: 0.8318 (m-30) cc_final: 0.7957 (m-30) REVERT: C 81 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 11 ASP cc_start: 0.8661 (m-30) cc_final: 0.8205 (m-30) REVERT: D 53 GLU cc_start: 0.7690 (tt0) cc_final: 0.7213 (tt0) REVERT: F 53 GLU cc_start: 0.7767 (tt0) cc_final: 0.7294 (tt0) REVERT: G 53 GLU cc_start: 0.7485 (tt0) cc_final: 0.7116 (tt0) REVERT: H 81 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8490 (tm-30) REVERT: I 53 GLU cc_start: 0.7739 (tt0) cc_final: 0.7231 (tt0) REVERT: I 81 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8458 (tm-30) REVERT: J 53 GLU cc_start: 0.7742 (tt0) cc_final: 0.7484 (tt0) REVERT: K 53 GLU cc_start: 0.7823 (tt0) cc_final: 0.7332 (tt0) REVERT: M 53 GLU cc_start: 0.7755 (tt0) cc_final: 0.7491 (tt0) REVERT: N 11 ASP cc_start: 0.8558 (m-30) cc_final: 0.8206 (m-30) REVERT: N 81 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8513 (tm-30) REVERT: P 81 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8400 (tm-30) REVERT: Q 53 GLU cc_start: 0.7787 (tt0) cc_final: 0.7404 (tt0) REVERT: S 53 GLU cc_start: 0.7735 (tt0) cc_final: 0.7338 (tt0) REVERT: T 53 GLU cc_start: 0.7608 (tt0) cc_final: 0.7092 (tt0) REVERT: U 81 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8537 (tm-30) REVERT: V 53 GLU cc_start: 0.7765 (tt0) cc_final: 0.7356 (tt0) REVERT: V 81 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8311 (tm-30) REVERT: W 53 GLU cc_start: 0.7686 (tt0) cc_final: 0.7174 (tt0) REVERT: X 81 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8487 (tm-30) REVERT: Y 53 GLU cc_start: 0.7712 (tt0) cc_final: 0.7146 (tt0) REVERT: 0 35 ARG cc_start: 0.9050 (ttt90) cc_final: 0.8754 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7716 (tt0) cc_final: 0.7309 (tt0) REVERT: 0 74 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7724 (ttp-170) REVERT: 0 81 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8441 (tm-30) REVERT: 1 53 GLU cc_start: 0.7700 (tt0) cc_final: 0.7234 (tt0) REVERT: 1 74 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7835 (ttp80) REVERT: 1 81 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8406 (tm-30) REVERT: 2 53 GLU cc_start: 0.7683 (tt0) cc_final: 0.7205 (tt0) REVERT: 2 74 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7775 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8383 (tm-30) REVERT: 3 81 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8459 (tm-30) outliers start: 50 outliers final: 45 residues processed: 380 average time/residue: 0.3152 time to fit residues: 190.2265 Evaluate side-chains 393 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 348 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 8 MET Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 8 MET Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Z residue 78 ILE Chi-restraints excluded: chain 0 residue 78 ILE Chi-restraints excluded: chain 2 residue 78 ILE Chi-restraints excluded: chain 3 residue 8 MET Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 78 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 80 ASN ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23040 Z= 0.213 Angle : 0.490 5.922 30990 Z= 0.257 Chirality : 0.035 0.215 3870 Planarity : 0.004 0.046 3150 Dihedral : 36.383 179.629 4950 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.29 % Allowed : 17.86 % Favored : 79.85 % 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: 4.41 (0.17), residues: 2460 helix: 2.91 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.47 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 28 PHE 0.012 0.002 PHE C 69 ARG 0.011 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 2.196 Fit side-chains REVERT: A 54 ASP cc_start: 0.8282 (m-30) cc_final: 0.7914 (m-30) REVERT: C 81 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 11 ASP cc_start: 0.8646 (m-30) cc_final: 0.8198 (m-30) REVERT: D 53 GLU cc_start: 0.7680 (tt0) cc_final: 0.7228 (tt0) REVERT: D 80 ASN cc_start: 0.9050 (t0) cc_final: 0.8796 (t0) REVERT: F 53 GLU cc_start: 0.7780 (tt0) cc_final: 0.7224 (tt0) REVERT: G 53 GLU cc_start: 0.7444 (tt0) cc_final: 0.7079 (tt0) REVERT: H 81 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8501 (tm-30) REVERT: I 53 GLU cc_start: 0.7697 (tt0) cc_final: 0.7186 (tt0) REVERT: I 81 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8449 (tm-30) REVERT: J 53 GLU cc_start: 0.7737 (tt0) cc_final: 0.7482 (tt0) REVERT: K 53 GLU cc_start: 0.7819 (tt0) cc_final: 0.7300 (tt0) REVERT: M 53 GLU cc_start: 0.7741 (tt0) cc_final: 0.7481 (tt0) REVERT: N 81 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8510 (tm-30) REVERT: P 81 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8393 (tm-30) REVERT: Q 53 GLU cc_start: 0.7735 (tt0) cc_final: 0.7344 (tt0) REVERT: S 53 GLU cc_start: 0.7779 (tt0) cc_final: 0.7403 (tt0) REVERT: T 53 GLU cc_start: 0.7631 (tt0) cc_final: 0.7217 (tt0) REVERT: U 81 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8555 (tm-30) REVERT: V 53 GLU cc_start: 0.7749 (tt0) cc_final: 0.7330 (tt0) REVERT: V 81 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8276 (tm-30) REVERT: W 53 GLU cc_start: 0.7632 (tt0) cc_final: 0.7168 (tt0) REVERT: X 81 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8480 (tm-30) REVERT: Y 53 GLU cc_start: 0.7702 (tt0) cc_final: 0.7138 (tt0) REVERT: 0 35 ARG cc_start: 0.9042 (ttt90) cc_final: 0.8738 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7702 (tt0) cc_final: 0.7297 (tt0) REVERT: 0 74 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7728 (ttp-170) REVERT: 1 53 GLU cc_start: 0.7673 (tt0) cc_final: 0.7218 (tt0) REVERT: 1 74 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7828 (ttp80) REVERT: 1 81 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8404 (tm-30) REVERT: 2 53 GLU cc_start: 0.7701 (tt0) cc_final: 0.7176 (tt0) REVERT: 2 74 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7742 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8385 (tm-30) REVERT: 3 81 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 46 outliers final: 37 residues processed: 369 average time/residue: 0.3142 time to fit residues: 185.8374 Evaluate side-chains 378 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 341 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain 0 residue 78 ILE Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 78 ILE Chi-restraints excluded: chain 3 residue 8 MET Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 80 ASN ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23040 Z= 0.247 Angle : 0.515 5.189 30990 Z= 0.267 Chirality : 0.035 0.212 3870 Planarity : 0.004 0.053 3150 Dihedral : 36.342 178.389 4950 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.64 % Allowed : 17.31 % Favored : 80.05 % 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: 4.37 (0.17), residues: 2460 helix: 2.88 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.54 (0.70), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 28 PHE 0.015 0.002 PHE C 69 ARG 0.012 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 350 time to evaluate : 2.237 Fit side-chains REVERT: A 54 ASP cc_start: 0.8356 (m-30) cc_final: 0.7976 (m-30) REVERT: C 81 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 7 GLN cc_start: 0.8148 (tp40) cc_final: 0.7841 (tp40) REVERT: D 53 GLU cc_start: 0.7702 (tt0) cc_final: 0.7240 (tt0) REVERT: D 80 ASN cc_start: 0.9055 (t0) cc_final: 0.8849 (t0) REVERT: F 53 GLU cc_start: 0.7788 (tt0) cc_final: 0.7243 (tt0) REVERT: G 53 GLU cc_start: 0.7496 (tt0) cc_final: 0.7129 (tt0) REVERT: H 81 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8545 (tm-30) REVERT: I 53 GLU cc_start: 0.7709 (tt0) cc_final: 0.7191 (tt0) REVERT: I 81 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8486 (tm-30) REVERT: J 53 GLU cc_start: 0.7776 (tt0) cc_final: 0.7523 (tt0) REVERT: K 53 GLU cc_start: 0.7812 (tt0) cc_final: 0.7279 (tt0) REVERT: L 53 GLU cc_start: 0.7730 (tt0) cc_final: 0.7246 (tt0) REVERT: M 53 GLU cc_start: 0.7809 (tt0) cc_final: 0.7583 (tt0) REVERT: N 11 ASP cc_start: 0.8562 (m-30) cc_final: 0.8224 (m-30) REVERT: N 81 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8513 (tm-30) REVERT: P 81 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8388 (tm-30) REVERT: Q 53 GLU cc_start: 0.7823 (tt0) cc_final: 0.7422 (tt0) REVERT: S 53 GLU cc_start: 0.7797 (tt0) cc_final: 0.7400 (tt0) REVERT: T 53 GLU cc_start: 0.7630 (tt0) cc_final: 0.7237 (tt0) REVERT: U 81 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8553 (tm-30) REVERT: V 53 GLU cc_start: 0.7752 (tt0) cc_final: 0.7340 (tt0) REVERT: V 81 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8281 (tm-30) REVERT: W 53 GLU cc_start: 0.7653 (tt0) cc_final: 0.7176 (tt0) REVERT: X 81 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8500 (tm-30) REVERT: Y 53 GLU cc_start: 0.7794 (tt0) cc_final: 0.7441 (tt0) REVERT: Z 53 GLU cc_start: 0.7876 (tt0) cc_final: 0.7270 (tt0) REVERT: 0 35 ARG cc_start: 0.9038 (ttt90) cc_final: 0.8754 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7720 (tt0) cc_final: 0.7481 (tt0) REVERT: 0 74 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7735 (ttp-170) REVERT: 0 81 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8482 (tm-30) REVERT: 1 53 GLU cc_start: 0.7699 (tt0) cc_final: 0.7225 (tt0) REVERT: 1 74 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7837 (ttp80) REVERT: 1 81 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8425 (tm-30) REVERT: 2 53 GLU cc_start: 0.7763 (tt0) cc_final: 0.7228 (tt0) REVERT: 2 74 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7738 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8372 (tm-30) REVERT: 3 81 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8459 (tm-30) outliers start: 53 outliers final: 46 residues processed: 373 average time/residue: 0.3266 time to fit residues: 191.2564 Evaluate side-chains 389 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 343 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain U residue 8 MET Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 8 MET Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain Y residue 78 ILE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain 0 residue 78 ILE Chi-restraints excluded: chain 0 residue 82 VAL Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 78 ILE Chi-restraints excluded: chain 2 residue 78 ILE Chi-restraints excluded: chain 3 residue 8 MET Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 78 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23040 Z= 0.168 Angle : 0.464 5.164 30990 Z= 0.247 Chirality : 0.033 0.191 3870 Planarity : 0.005 0.062 3150 Dihedral : 35.643 179.633 4950 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.95 % Allowed : 19.30 % Favored : 79.75 % 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: 4.63 (0.17), residues: 2460 helix: 3.04 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.66 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 28 PHE 0.005 0.001 PHE C 69 ARG 0.013 0.001 ARG N 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 350 time to evaluate : 2.327 Fit side-chains REVERT: A 54 ASP cc_start: 0.8262 (m-30) cc_final: 0.7898 (m-30) REVERT: A 81 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8788 (tm-30) REVERT: C 81 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8417 (tm-30) REVERT: D 53 GLU cc_start: 0.7626 (tt0) cc_final: 0.7163 (tt0) REVERT: F 33 THR cc_start: 0.9090 (m) cc_final: 0.8890 (m) REVERT: F 53 GLU cc_start: 0.7722 (tt0) cc_final: 0.7160 (tt0) REVERT: H 81 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8515 (tm-30) REVERT: I 53 GLU cc_start: 0.7635 (tt0) cc_final: 0.7132 (tt0) REVERT: I 81 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8457 (tm-30) REVERT: J 53 GLU cc_start: 0.7658 (tt0) cc_final: 0.7404 (tt0) REVERT: K 53 GLU cc_start: 0.7787 (tt0) cc_final: 0.7321 (tt0) REVERT: N 81 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8582 (tm-30) REVERT: P 81 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8365 (tm-30) REVERT: Q 53 GLU cc_start: 0.7552 (tt0) cc_final: 0.7239 (tt0) REVERT: T 81 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8529 (tm-30) REVERT: U 81 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8556 (tm-30) REVERT: V 53 GLU cc_start: 0.7652 (tt0) cc_final: 0.7257 (tt0) REVERT: V 81 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8288 (tm-30) REVERT: W 53 GLU cc_start: 0.7551 (tt0) cc_final: 0.7092 (tt0) REVERT: X 81 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8525 (tm-30) REVERT: Y 53 GLU cc_start: 0.7727 (tt0) cc_final: 0.7300 (tt0) REVERT: Z 81 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8603 (tm-30) REVERT: 0 35 ARG cc_start: 0.9051 (ttt90) cc_final: 0.8720 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7659 (tt0) cc_final: 0.7240 (tt0) REVERT: 0 74 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7729 (ttp80) REVERT: 0 81 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8482 (tm-30) REVERT: 1 74 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7802 (ttp-170) REVERT: 1 81 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8463 (tm-30) REVERT: 2 53 GLU cc_start: 0.7619 (tt0) cc_final: 0.7083 (tt0) REVERT: 2 74 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7772 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8411 (tm-30) REVERT: 3 81 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8419 (tm-30) outliers start: 19 outliers final: 13 residues processed: 356 average time/residue: 0.2875 time to fit residues: 168.7463 Evaluate side-chains 344 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23040 Z= 0.171 Angle : 0.464 5.142 30990 Z= 0.248 Chirality : 0.033 0.188 3870 Planarity : 0.005 0.051 3150 Dihedral : 35.491 179.827 4950 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.80 % Allowed : 20.60 % Favored : 78.61 % 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: 4.71 (0.17), residues: 2460 helix: 3.08 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.95 (0.72), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 28 PHE 0.015 0.001 PHE K 69 ARG 0.012 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 326 time to evaluate : 2.248 Fit side-chains REVERT: A 54 ASP cc_start: 0.8263 (m-30) cc_final: 0.7891 (m-30) REVERT: A 81 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8812 (tm-30) REVERT: C 81 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8421 (tm-30) REVERT: D 53 GLU cc_start: 0.7599 (tt0) cc_final: 0.7175 (tt0) REVERT: F 33 THR cc_start: 0.9131 (m) cc_final: 0.8923 (m) REVERT: F 53 GLU cc_start: 0.7720 (tt0) cc_final: 0.7312 (tt0) REVERT: H 81 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8546 (tm-30) REVERT: I 53 GLU cc_start: 0.7629 (tt0) cc_final: 0.7142 (tt0) REVERT: I 81 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8500 (tm-30) REVERT: J 53 GLU cc_start: 0.7653 (tt0) cc_final: 0.7398 (tt0) REVERT: K 53 GLU cc_start: 0.7796 (tt0) cc_final: 0.7333 (tt0) REVERT: N 81 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8570 (tm-30) REVERT: P 81 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8395 (tm-30) REVERT: Q 53 GLU cc_start: 0.7531 (tt0) cc_final: 0.7210 (tt0) REVERT: T 81 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8536 (tm-30) REVERT: U 81 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8598 (tm-30) REVERT: V 53 GLU cc_start: 0.7651 (tt0) cc_final: 0.7253 (tt0) REVERT: V 81 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8337 (tm-30) REVERT: W 53 GLU cc_start: 0.7536 (tt0) cc_final: 0.7085 (tt0) REVERT: X 81 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8530 (tm-30) REVERT: Y 53 GLU cc_start: 0.7734 (tt0) cc_final: 0.7294 (tt0) REVERT: Z 81 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8607 (tm-30) REVERT: 0 35 ARG cc_start: 0.9060 (ttt90) cc_final: 0.8729 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7646 (tt0) cc_final: 0.7220 (tt0) REVERT: 0 74 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7751 (ttp80) REVERT: 0 81 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8519 (tm-30) REVERT: 1 74 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7803 (ttp-170) REVERT: 1 81 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8575 (tm-30) REVERT: 2 53 GLU cc_start: 0.7617 (tt0) cc_final: 0.7077 (tt0) REVERT: 2 74 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7800 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8454 (tm-30) REVERT: 3 81 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8468 (tm-30) outliers start: 16 outliers final: 11 residues processed: 332 average time/residue: 0.2858 time to fit residues: 157.3790 Evaluate side-chains 329 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 318 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23040 Z= 0.330 Angle : 0.575 5.587 30990 Z= 0.296 Chirality : 0.036 0.231 3870 Planarity : 0.005 0.046 3150 Dihedral : 36.250 179.984 4950 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.90 % Allowed : 20.85 % Favored : 78.26 % 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: 4.43 (0.17), residues: 2460 helix: 2.90 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : 2.88 (0.72), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 28 PHE 0.019 0.002 PHE C 69 ARG 0.012 0.001 ARG Q 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 348 time to evaluate : 2.427 Fit side-chains REVERT: B 53 GLU cc_start: 0.7722 (tt0) cc_final: 0.7226 (tt0) REVERT: A 54 ASP cc_start: 0.8437 (m-30) cc_final: 0.8122 (m-30) REVERT: A 81 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 81 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 7 GLN cc_start: 0.8215 (tp40) cc_final: 0.8008 (tp40) REVERT: D 53 GLU cc_start: 0.7801 (tt0) cc_final: 0.7326 (tt0) REVERT: F 53 GLU cc_start: 0.7832 (tt0) cc_final: 0.7277 (tt0) REVERT: G 53 GLU cc_start: 0.7550 (tt0) cc_final: 0.7168 (tt0) REVERT: H 81 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8548 (tm-30) REVERT: I 53 GLU cc_start: 0.7756 (tt0) cc_final: 0.7217 (tt0) REVERT: I 81 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8532 (tm-30) REVERT: J 53 GLU cc_start: 0.7825 (tt0) cc_final: 0.7584 (tt0) REVERT: K 53 GLU cc_start: 0.7808 (tt0) cc_final: 0.7326 (tt0) REVERT: L 11 ASP cc_start: 0.8929 (m-30) cc_final: 0.8441 (m-30) REVERT: L 53 GLU cc_start: 0.7755 (tt0) cc_final: 0.7211 (tt0) REVERT: M 53 GLU cc_start: 0.7846 (tt0) cc_final: 0.7331 (tt0) REVERT: N 7 GLN cc_start: 0.8270 (tp40) cc_final: 0.7883 (tp40) REVERT: N 11 ASP cc_start: 0.8536 (m-30) cc_final: 0.8208 (m-30) REVERT: N 53 GLU cc_start: 0.7677 (tt0) cc_final: 0.7119 (tt0) REVERT: N 81 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8590 (tm-30) REVERT: P 81 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8404 (tm-30) REVERT: Q 7 GLN cc_start: 0.8167 (tp40) cc_final: 0.7661 (tp40) REVERT: Q 11 ASP cc_start: 0.8775 (m-30) cc_final: 0.8451 (m-30) REVERT: Q 53 GLU cc_start: 0.7797 (tt0) cc_final: 0.7419 (tt0) REVERT: S 53 GLU cc_start: 0.7892 (tt0) cc_final: 0.7460 (tt0) REVERT: T 53 GLU cc_start: 0.7731 (tt0) cc_final: 0.7332 (tt0) REVERT: U 81 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8616 (tm-30) REVERT: V 53 GLU cc_start: 0.7772 (tt0) cc_final: 0.7368 (tt0) REVERT: V 81 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8287 (tm-30) REVERT: W 53 GLU cc_start: 0.7687 (tt0) cc_final: 0.7247 (tt0) REVERT: W 81 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8613 (tm-30) REVERT: X 81 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8547 (tm-30) REVERT: Y 53 GLU cc_start: 0.7827 (tt0) cc_final: 0.7464 (tt0) REVERT: Z 53 GLU cc_start: 0.7896 (tt0) cc_final: 0.7299 (tt0) REVERT: 0 35 ARG cc_start: 0.9025 (ttt90) cc_final: 0.8795 (ttt-90) REVERT: 0 53 GLU cc_start: 0.7776 (tt0) cc_final: 0.7496 (tt0) REVERT: 0 74 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7836 (ttp-170) REVERT: 0 81 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8559 (tm-30) REVERT: 1 53 GLU cc_start: 0.7747 (tt0) cc_final: 0.7322 (tt0) REVERT: 1 74 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7826 (ttp80) REVERT: 1 81 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8486 (tm-30) REVERT: 2 53 GLU cc_start: 0.7773 (tt0) cc_final: 0.7247 (tt0) REVERT: 2 74 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7740 (ttp-170) REVERT: 2 81 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8457 (tm-30) REVERT: 3 81 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8466 (tm-30) outliers start: 18 outliers final: 14 residues processed: 355 average time/residue: 0.3633 time to fit residues: 197.5223 Evaluate side-chains 357 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 343 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain V residue 56 MET Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain 3 residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086986 restraints weight = 35936.049| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.62 r_work: 0.2880 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23040 Z= 0.200 Angle : 0.504 6.099 30990 Z= 0.266 Chirality : 0.034 0.201 3870 Planarity : 0.006 0.065 3150 Dihedral : 35.859 178.642 4950 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.40 % Allowed : 21.69 % Favored : 77.91 % 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: 4.56 (0.17), residues: 2460 helix: 3.09 (0.10), residues: 2310 sheet: None (None), residues: 0 loop : 1.08 (0.63), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 28 PHE 0.009 0.001 PHE C 69 ARG 0.014 0.001 ARG Q 46 =============================================================================== Job complete usr+sys time: 4146.25 seconds wall clock time: 75 minutes 12.34 seconds (4512.34 seconds total)